bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of extreme summers on European ecosystems: a comparative analysis of 2003, 2010 and 2018
Authors: Bastos A. , Fu Z. , Ciais P. , Friedlingstein P. , Sitch S. , Pongratz J. , Weber U. , Reichstein M. , Anthoni P. , Arneth A. , Haverd V. , Jain A. , Joetzjer E. , Knauer J. , Lienert S. , Loughran T. , McGuire P. C. , Obermeier W. , Padrón R. S. , Shi H. , Tian H. , Viovy N. , Zaehle S.
Published: September 2020

In Europe, three widespread extreme summer drought and heat (DH) events have occurred in 2003, 2010 and 2018. These events were comparable in magnitude but varied in their geographical distribution and biomes affected. In this study, we perform a comparative analysis of the impact of the DH events on ecosystem CO2fluxes over Europe based on an ensemble of 11 dynamic global vegetation models (DGVMs), and the observation-based FLUXCOM product. We find that all DH events were associated with decreases in net ecosystem productivity (NEP), but the gross summer flux anomalies differ between DGVMs and FLUXCOM. At the annual scale, FLUXCOM and DGVMs indicate close to neutral or above-average land CO2uptake in DH2003 and DH2018, due to increased productivity in spring and reduced respiration in autumn and winter compensating for less photosynthetic uptake in summer. Most DGVMs estimate lower gross primary production (GPP) sensitivity to soil moisture during extreme summers than FLUXCOM. Finally, we show that the different impacts of the DH events at continental-scale GPP are in part related to differences in vegetation composition of the regions affected and to regional compensating or offsetting effects from climate anomalies beyond the DH centres.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Spring enhancement and summer reduction in carbon uptake during the 2018 drought in northwestern Europe
Authors: Smith Naomi E. , Kooijmans Linda M. J. , Koren Gerbrand , van Schaik Erik , van der Woude Auke M. , Wanders Niko , Ramonet Michel , Xueref-Remy Irène , Siebicke Lukas , Manca Giovanni , Brümmer Christian , Baker Ian T. , Haynes Katherine D. , Luijkx Ingrid T. , Peters Wouter
Published: September 2020

We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide (CO2) by the terrestrial biosphere during the summer of 2018 through observed changes across the Integrated Carbon Observation System (ICOS) network, through biosphere and inverse modelling, and through remote sensing. Highly correlated yet independently-derived reductions in productivity from sun-induced fluorescence, vegetative near-infrared reflectance, and GPP simulated by the Simple Biosphere model version 4 (SiB4) suggest a 130–340 TgC GPP reduction in July–August–September (JAS) of 2018. This occurs over an area of 1.6 × 106km2with anomalously low precipitation in northwestern and central Europe. In this drought-affected area, reduced GPP, TER, NEE and soil moisture at ICOS ecosystem sites are reproduced satisfactorily by the SiB4 model. We found that, in contrast to the preceding 5 years, low soil moisture is the main stress factor across the affected area. SiB4’s NEE reduction by 57 TgC for JAS coincides with anomalously high atmospheric CO2observations in 2018, and this is closely matched by the NEE anomaly derived by CarbonTracker Europe (52 to 83 TgC). Increased NEE during the spring (May–June) of 2018 (SiB4 −52 TgC; CTE −46 to −55 TgC) largely offset this loss, as ecosystems took advantage of favourable growth conditions.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Impact of extreme weather conditions on European crop production in 2018
Authors: Beillouin Damien , Schauberger Bernhard , Bastos Ana , Ciais Phillipe , Makowski David
Published: September 2020

Extreme weather increases the risk of large-scale crop failure. The mechanisms involved are complex and intertwined, hence undermining the identification of simple adaptation levers to help improve the resilience of agricultural production. Based on more than 82 000 yield data reported at the regional level in 17 European countries, we assess how climate affected the yields of nine crop species. Using machine learning models, we analyzed historical yield data since 1901 and then focus on 2018, which has experienced a multiplicity and a diversity of atypical extreme climatic conditions. Machine learning models explain up to 65% of historical yield anomalies. We find that both extremes in temperature and precipitation are associated with negative yield anomalies, but with varying impacts in different parts of Europe. In 2018, Northern and Eastern Europe experienced multiple and simultaneous crop failures—among the highest observed in recent decades. These yield losses were associated with extremely low rainfalls in combination with high temperatures between March and August 2018. However, the higher than usual yields recorded in Southern Europe—caused by favourable spring rainfall conditions—nearly offset the large decrease in Northern European crop production. Our results outline the importance of considering single and compound climate extremes to analyse the causes of yield losses in Europe. We found no clear upward or downward trend in the frequency of extreme yield losses for any of the considered crops between 1990 and 2018.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.
Changes in net ecosystem exchange over Europe during the 2018 drought based on atmospheric observations
Authors: Thompson R. L. , Broquet G. , Gerbig C. , Koch T. , Lang M. , Monteil G. , Munassar S. , Nickless A. , Scholze M. , Ramonet M. , Karstens U. , van Schaik E. , Wu Z. , Rödenbeck C.
Published: September 2020

The 2018 drought was one of the worst European droughts of the twenty-first century in terms of its severity, extent and duration. The effects of the drought could be seen in a reduction in harvest yields in parts of Europe, as well as an unprecedented browning of vegetation in summer. Here, we quantify the effect of the drought on net ecosystem exchange (NEE) using five independent regional atmospheric inversion frameworks. Using a network of atmospheric CO
2
mole fraction observations, we estimate NEE with at least monthly and 0.5° × 0.5° resolution for 2009–2018. We find that the annual NEE in 2018 was likely more positive (less CO
2
uptake) in the temperate region of Europe by 0.09 ± 0.06 Pg C yr
−1
(mean ± s.d.) compared to the mean of the last 10 years of −0.08 ± 0.17 Pg C yr
−1
, making the region close to carbon neutral in 2018. Similarly, we find a positive annual NEE anomaly for the northern region of Europe of 0.02 ± 0.02 Pg C yr
−1
compared the 10-year mean of −0.04 ± 0.05 Pg C yr
−1
. In both regions, this was largely owing to a reduction in the summer CO
2
uptake. The positive NEE anomalies coincided spatially and temporally with negative anomalies in soil water. These anomalies were exceptional for the 10-year period of our study.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Effects of drought and meteorological forcing on carbon and water fluxes in Nordic forests during the dry summer of 2018
Authors: Lindroth Anders , Holst Jutta , Linderson Maj-Lena , Aurela Mika , Biermann Tobias , Heliasz Michal , Chi Jinshu , Ibrom Andreas , Kolari Pasi , Klemedtsson Leif , Krasnova Alisa , Laurila Tuomas , Lehner Irene , Lohila Annalea , Mammarella Ivan , Mölder Meelis , Löfvenius Mikaell Ottosson , Peichl Matthias , Pilegaard Kim , Soosaar Kaido , Vesala Timo , Vestin Patrik , Weslien Per , Nilsson Mats
Published: September 2020

The Nordic region was subjected to severe drought in 2018 with a particularly long-lasting and large soil water deficit in Denmark, Southern Sweden and Estonia. Here, we analyse the impact of the drought on carbon and water fluxes in 11 forest ecosystems of different composition: spruce, pine, mixed and deciduous. We assess the impact of drought on fluxes by estimating the difference (anomaly) between year 2018 and a reference year without drought. Unexpectedly, the evaporation was only slightly reduced during 2018 compared to the reference year at two sites while it increased or was nearly unchanged at all other sites. This occurred under a 40 to 60% reduction in mean surface conductance and the concurrent increase in evaporative demand due to the warm and dry weather. The anomaly in the net ecosystem productivity (NEP) was 93% explained by a multilinear regression with the anomaly in heterotrophic respiration and the relative precipitation deficit as independent variables. Most of the variation (77%) was explained by the heterotrophic component. Six out of 11 forests reduced their annual NEP with more than 50 g C m
−2
yr
−1
during 2018 as compared to the reference year. The NEP anomaly ranged between −389 and +74 g C m
−2
yr
−1
with a median value of −59 g C m
−2
yr
−1
.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Effect of the 2018 European drought on methane and carbon dioxide exchange of northern mire ecosystems
Authors: Rinne J. , Tuovinen J.-P. , Klemedtsson L. , Aurela M. , Holst J. , Lohila A. , Weslien P. , Vestin P. , Łakomiec P. , Peichl M. , Tuittila E.-S. , Heiskanen L. , Laurila T. , Li X. , Alekseychik P. , Mammarella I. , Ström L. , Crill P. , Nilsson M. B.
Published: September 2020

We analysed the effect of the 2018 European drought on greenhouse gas (GHG) exchange of five North European mire ecosystems. The low precipitation and high summer temperatures in Fennoscandia led to a lowered water table in the majority of these mires. This lowered both carbon dioxide (CO
2
) uptake and methane (CH
4
) emission during 2018, turning three out of the five mires from CO
2
sinks to sources. The calculated radiative forcing showed that the drought-induced changes in GHG fluxes first resulted in a cooling effect lasting 15–50 years, due to the lowered CH
4
emission, which was followed by warming due to the lower CO
2
uptake.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Analysis of floodplain forest sensitivity to drought
Authors: Kowalska Natalia , Šigut Ladislav , Stojanović Marko , Fischer Milan , Kyselova Ina , Pavelka Marian
Published: September 2020

Floodplain forests are very complex, productive ecosystems, capable of storing huge amounts of soil carbon. With the increasing occurrence of extreme events, they are today among the most threatened ecosystems. Our study's main goal was to assess the productivity of a floodplain forest located at Lanžhot in the Czech Republic from two perspectives: carbon uptake (using an eddy covariance method) and stem radius variations (using dendrometers). We aimed to determine which conditions allow for high ecosystem production and what role drought plays in reducing such production potential. Additionally, we were interested to determine the relative soil water content threshold indicating the onset and duration of this event. We hypothesized that summer drought in 2018 had the most significant negative effects on the overall annual carbon and water budgets. In contrast with our original hypothesis, we found that an exceptionally warm spring in 2018 caused a positive gross primary production (GPP) and evapotranspiration (ET) anomaly that consequently led in 2018 to the highest seasonal total GPP and ET from all of the investigated years (2015–2018). The results showed ring-porous species to be the most drought resistant. Relative soil water content threshold of approximately 0.45 was determined as indicating the onset of drought stress.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Drought and heatwave impacts on semi-arid ecosystems' carbon fluxes along a precipitation gradient
Authors: El-Madany Tarek S. , Carrara Arnaud , Martín M. Pilar , Moreno Gerardo , Kolle Olaf , Pacheco-Labrador Javier , Weber Ulrich , Wutzler Thomas , Reichstein Markus , Migliavacca Mirco
Published: September 2020

The inter-annual variability (IAV) of the terrestrial carbon cycle is tightly linked to the variability of semi-arid ecosystems. Thus, it is of utmost importance to understand what the main meteorological drivers for the IAV of such ecosystems are, and how they respond to extreme events such as droughts and heatwaves. To shed light onto these questions, we analyse the IAV of carbon fluxes, its relation with meteorological variables, and the impact of compound drought and heatwave on the carbon cycle of two similar ecosystems, along a precipitation gradient. A four-year long dataset from 2016 to 2019 was used for the FLUXNET sites ES-LMa and ES-Abr, located in central (39°56'25″ N 5°46'28″ W) and southeastern (38°42'6″ N 6°47'9″ W) Spain. We analyse the physiological impact of compound drought and heatwave on the dominant tree species,
Quercus ilex.
Our results show that the gross primary productivity of the wetter ecosystem was less sensitive to changes in soil water content, compared to the dryer site. Still, the wetter ecosystem was a source of CO
2
each year, owing to large ecosystem respiration during summer; while the dry site turned into a CO
2
sink during wet years. Overall, the impact of the summertime compound event on annual CO
2
fluxes was marginal at both sites, compared to drought events during spring or autumn. This highlights that drought timing is crucial to determine the annual carbon fluxes in these semi-arid ecosystems.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Physiological response of Swiss ecosystems to 2018 drought across plant types and elevation
Authors: Gharun Mana , Hörtnagl Lukas , Paul-Limoges Eugénie , Ghiasi Shiva , Feigenwinter Iris , Burri Susanne , Marquardt Kristiina , Etzold Sophia , Zweifel Roman , Eugster Werner , Buchmann Nina
Published: September 2020

Using five eddy covariance flux sites (two forests and three grasslands), we investigated ecosystem physiological responses to the 2018 drought across elevational gradients in Switzerland. Flux measurements showed that at lower elevation sites (below 1000 m.a.s.l.; grassland and mixed forest) annual ecosystem productivity (GPP) declined by approximately 20% compared to the previous 2 years (2016 and 2017), which led to a reduced annual net ecosystem productivity (NEP). At the high elevation sites, however, GPP increased by approximately 14% and as a result NEP increased in the alpine and montane grasslands, but not in the subalpine coniferous forest. There, increased ecosystem respiration led to a reduced annual NEP, despite increased GPP and lengthening of the growing period. Among all ecosystems, the coniferous forest showed the most pronounced negative stomatal response to atmospheric dryness (i.e. vapour pressure deficit, VPD) that resulted in a decline in surface conductance and an increased water-use efficiency during drought. While increased temperature enhanced the water-use efficiency of both forests, de-coupling of GPP from evapotranspiration at the low-elevation grassland site negatively affected water-use efficiency due to non-stomatal reductions in photosynthesis. Our results show that hot droughts (such as in 2018) lead to different responses across plants types, and thus ecosystems. Particularly grasslands at lower elevations are the most vulnerable ecosystems to negative impacts of future drought in Switzerland.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Altered energy partitioning across terrestrial ecosystems in the European drought year 2018
Authors: Graf Alexander , Klosterhalfen Anne , Arriga Nicola , Bernhofer Christian , Bogena Heye , Bornet Frédéric , Brüggemann Nicolas , Brümmer Christian , Buchmann Nina , Chi Jinshu , Chipeaux Christophe , Cremonese Edoardo , Cuntz Matthias , Dušek Jiří , El-Madany Tarek S. , Fares Silvano , Fischer Milan , Foltýnová Lenka , Gharun Mana , Ghiasi Shiva , Gielen Bert , Gottschalk Pia , Grünwald Thomas , Heinemann Günther , Heinesch Bernard , Heliasz Michal , Holst Jutta , Hörtnagl Lukas , Ibrom Andreas , Ingwersen Joachim , Jurasinski Gerald , Klatt Janina , Knohl Alexander , Koebsch Franziska , Konopka Jan , Korkiakoski Mika , Kowalska Natalia , Kremer Pascal , Kruijt Bart , Lafont Sebastien , Léonard Joël , De Ligne Anne , Longdoz Bernard , Loustau Denis , Magliulo Vincenzo , Mammarella Ivan , Manca Giovanni , Mauder Matthias , Migliavacca Mirco , Mölder Meelis , Neirynck Johan , Ney Patrizia , Nilsson Mats , Paul-Limoges Eugénie , Peichl Matthias , Pitacco Andrea , Poyda Arne , Rebmann Corinna , Roland Marilyn , Sachs Torsten , Schmidt Marius , Schrader Frederik , Siebicke Lukas , Šigut Ladislav , Tuittila Eeva-Stiina , Varlagin Andrej , Vendrame Nadia , Vincke Caroline , Völksch Ingo , Weber Stephan , Wille Christian , Wizemann Hans-Dieter , Zeeman Matthias , Vereecken Harry
Published: September 2020

Drought and heat events, such as the 2018 European drought, interact with the exchange of energy between the land surface and the atmosphere, potentially affecting albedo, sensible and latent heat fluxes, as well as CO
2
exchange. Each of these quantities may aggravate or mitigate the drought, heat, their side effects on productivity, water scarcity and global warming. We used measurements of 56 eddy covariance sites across Europe to examine the response of fluxes to extreme drought prevailing most of the year 2018 and how the response differed across various ecosystem types (forests, grasslands, croplands and peatlands). Each component of the surface radiation and energy balance observed in 2018 was compared to available data per site during a reference period 2004–2017. Based on anomalies in precipitation and reference evapotranspiration, we classified 46 sites as drought affected. These received on average 9% more solar radiation and released 32% more sensible heat to the atmosphere compared to the mean of the reference period. In general, drought decreased net CO
2
uptake by 17.8%, but did not significantly change net evapotranspiration. The response of these fluxes differed characteristically between ecosystems; in particular, the general increase in the evaporative index was strongest in peatlands and weakest in croplands.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Non-stomatal processes reduce gross primary productivity in temperate forest ecosystems during severe edaphic drought
Authors: Gourlez de la Motte Louis , Beauclaire Quentin , Heinesch Bernard , Cuntz Mathias , Foltýnová Lenka , Šigut Ladislav , Kowalska Natalia , Manca Giovanni , Ballarin Ignacio Goded , Vincke Caroline , Roland Marilyn , Ibrom Andreas , Lousteau Denis , Siebicke Lukas , Neiryink Johan , Longdoz Bernard
Published: September 2020

Severe drought events are known to cause important reductions of gross primary productivity (
GPP
) in forest ecosystems. However, it is still unclear whether this reduction originates from stomatal closure (Stomatal Origin Limitation) and/or non-stomatal limitations (Non-SOL). In this study, we investigated the impact of edaphic drought in 2018 on
GPP
and its origin (SOL, NSOL) using a dataset of 10 European forest ecosystem flux towers. In all stations where
GPP
reductions were observed during the drought, these were largely explained by declines in the maximum apparent canopy scale carboxylation rate
V
CMAX,APP
(NSOL) when the soil relative extractable water content dropped below around 0.4. Concurrently, we found that the stomatal slope parameter (

G
1

, related to SOL) of the Medlyn
et al
. unified optimization model linking vegetation conductance and
GPP
remained relatively constant. These results strengthen the increasing evidence that NSOL should be included in stomatal conductance/photosynthesis models to faithfully simulate both
GPP
and water fluxes in forest ecosystems during severe drought.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
The impact of occasional drought periods on vegetation spread and greenhouse gas exchange in rewetted fens
Authors: Koebsch Franziska , Gottschalk Pia , Beyer Florian , Wille Christian , Jurasinski Gerald , Sachs Torsten
Published: September 2020

Peatland rewetting aims at stopping the emissions of carbon dioxide (CO
2
) and establishing net carbon sinks. However, in times of global warming, restoration projects must increasingly deal with extreme events such as drought periods. Here, we evaluate the effect of the European summer drought 2018 on vegetation development and the exchange of methane (CH
4
) and CO
2
in two rewetted minerotrophic fens (Hütelmoor—Hte and Zarnekow—Zrk) including potential carry-over effects in the post-drought year. Drought was a major stress factor for the established vegetation but also promoted the rapid spread of new vegetation, which will likely gain a lasting foothold in Zrk. Accordingly, drought increased not only respiratory CO
2
losses but also photosynthetic CO
2
uptake. Altogether, the drought reduced the net CO
2
sink in Hte, while it stopped the persistent net CO
2
emissions of Zrk. In addition, the drought reduced CH
4
emissions in both fens, though this became most apparent in the post-drought year and suggests a lasting shift towards non-methanogenic organic matter decomposition. Occasional droughts can be beneficial for the restoration of the peatland carbon sink function if the newly grown vegetation increases CO
2
sequestration in the long term. Nonetheless, care must be taken to prevent extensive peat decay.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.
Sensitivity of gross primary productivity to climatic drivers during the summer drought of 2018 in Europe
Authors: Fu Zheng , Ciais Philippe , Bastos Ana , Stoy Paul C. , Yang Hui , Green Julia K. , Wang Bingxue , Yu Kailiang , Huang Yuanyuan , Knohl Alexander , Šigut Ladislav , Gharun Mana , Cuntz Matthias , Arriga Nicola , Roland Marilyn , Peichl Matthias , Migliavacca Mirco , Cremonese Edoardo , Varlagin Andrej , Brümmer Christian , Gourlez de la Motte Louis , Fares Silvano , Buchmann Nina , El-Madany Tarek S. , Pitacco Andrea , Vendrame Nadia , Li Zhaolei , Vincke Caroline , Magliulo Enzo , Koebsch Franziska
Published: September 2020

In summer 2018, Europe experienced a record drought, but it remains unknown how the drought affected ecosystem carbon dynamics. Using observations from 34 eddy covariance sites in different biomes across Europe, we studied the sensitivity of gross primary productivity (GPP) to environmental drivers during the summer drought of 2018 versus the reference summer of 2016. We found a greater drought-induced decline of summer GPP in grasslands (−38%) than in forests (−10%), which coincided with reduced evapotranspiration and soil water content (SWC). As compared to the ‘normal year’ of 2016, GPP in different ecosystems exhibited more negative sensitivity to summer air temperature (Ta) but stronger positive sensitivity to SWC during summer drought in 2018, that is, a stronger reduction of GPP with soil moisture deficit. We found larger negative effects of Ta and vapour pressure deficit (VPD) but a lower positive effect of photosynthetic photon flux density on GPP in 2018 compared to 2016, which contributed to reduced summer GPP in 2018. Our results demonstrate that high temperature-induced increases in VPD and decreases in SWC aggravated drought impacts on GPP.

This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Morphological stasis masks ecologically divergent coral species on tropical reefs
Authors: Bongaerts P , Cooke IR , Ying H , Wels D , Haan den S , Hernandez-Agreda A , Brunner CA , Dove S , Englebert N , Eyal G , Forêt S , Grinblat M , Hay KB , Harii S , Hayward DC , Lin Y , Mihaljević M , Moya A , Muir P , Sinniger F , Smallhorn-West P , Torda G , Ragan MA , van Oppen MJH , Hoegh-Guldberg O
Published: September 2020

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa), and uncover through a comprehensive genomic and phenotypic assessment that it comprises morphologically indistinguishable, but ecologically divergent cryptic lineages. Demographic modelling based on whole-genome resequencing disproved that morphological crypsis was due to recent divergence, and instead indicated ancient morphological stasis. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid diagnostic assay revealed differentiation of their ecological distributions. Leveraging “common garden” conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate how ecologically and phenotypically divergent coral species can evolve despite morphological stasis, and provide new leads into the potential mechanisms facilitating such divergence in sympatry. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.
Mutational landscapes of normal breast during age and pregnancy determine cancer risk
Authors: Cereser Biancastella , Tabassum Neha , Belluz Lisa Del Bel , Yiu Angela , Zagorac Sladjana , Miere Cristian , Werner Benjamin , Moderau Nina , Jeffries-Jones Alicia Rose , Stebbing Justin
Published: September 2020

The accumulation of somatic mutations in the healthy breast throughout life and pregnancy is poorly understood1–10. Similarly, the mutational landscape of both epithelial and stromal components of the mammary gland has not been investigated. Both are relevant for breast cancer (BC), as the interplay between age, pregnancy, and cancer risk has not been fully characterized11. We describe whole genome sequencing analysis of epithelial and stromal compartments from the normal breast. We show that, in a similar way to other normal organs, the mutational burden of the mammary nulliparous epithelium significantly increases with age. In a nulliparous status, mutated clones are maintained at a consistently small size throughout the life of the individual; however, at parity, pre-existent clones significantly increase in size with age. Both epithelial and stromal compartments of the healthy breast contain pre-existing known cancer mutations, albeit at low rate, indicative of subsequent positive selection for mutations in tissue-specific driver genes. In line with this, both compartments also present gene enrichment in preferentially mutated cancer pathways. Our results show that mutational landscapes differ between the parous and nulliparous epithelium and suggest an explanation for both differential breast cancer risk and development of pregnancy-associated BC (PABC).
Mosaic evolution of molecular pathways for sex pheromone communication in a butterfly
Authors: Nieberding Caroline M. , Beldade Patrícia , Baumlé Véronique , Martin Gilles San , Arun Alok , Lognay Georges , Montagné Nicolas , Bastin-Héline Lucie , Jacquin-Joly Emmanuelle , Noirot Céline , Klopp Christophe , Visser Bertanne
Published: September 2020

Unraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved, ancestral traits, and newly evolved, derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~98 million years ago. In moths, females typically emit pheromones to attract male mates, but in butterflies pheromones and used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but have remained virtually unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics, to identify genes involved in different steps of sex pheromone communication in the butterflyBicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly,B. anynanafurther appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulation of sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale analysis of the genetic pathways underlying sex pheromone communication in a butterfly.
3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk
Authors: Liu Ning , Sadlon Timothy , Wong Ying Ying , Pederson Stephen , Breen James , Barry Simon C
Published: September 2020

Background

Genome-wide association and fine-mapping studies have enabled the discovery of single nucleotide polymorphisms (SNPs) and other variants that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the SNPs lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression.

Methods

Autoimmunity results from a failure of immune tolerance, suggesting that regulatory T cells (Treg) are likely a significant point of impact for this genetic risk, as Treg are critical for immune tolerance. Focusing on T1D as a model of defective function of Treg in autoimmunity, we designed a SNPs filtering workflow called 3 Dimensional Functional Annotation of Accessible Cell Type Specific SNPs (3DFAACTS-SNP) that utilises overlapping profiles of Treg-specific epigenomic data (ATAC-seq, Hi-C and FOXP3-ChIP) to identify regulatory elements potentially driving the effect of variants associated with T1D, and the gene(s) that they control.

Results

Using 3DFAACTS-SNP we identified 36 SNPs with plausible Treg-specific mechanisms of action contributing to T1D from 1,228 T1D fine-mapped variants, identifying 119 novel interacting regions resulting in the identification of 51 candidate target genes. We further demonstrated the utility of the workflow by applying it to three other fine-mapped/meta-analysed SNP autoimmune datasets, identifying 17 Treg-centric candidate variants and 35 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of any genetic variation using all common (>10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 7,900 candidate variants and 3,245 candidate target genes, generating a list of potential sites for future T1D or autoimmune research.

Conclusions

We demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function and illustrate the power of using cell type specific multi-omics datasets to determine disease mechanisms. The 3DFAACTS-SNP workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility.
Frontotemporal dementia mutant tau (P301L) locks Fyn in an open, active conformation conducive to nanoclustering
Authors: Small Christopher , Martínez-Mármol Ramón , Wallis Tristan P. , Gormal Rachel S. , Götz Jürgen , Meunier Frédéric A.
Published: September 2020

Fyn is a Src kinase that controls critical signalling cascades and its postsynaptic enrichment underpins synaptotoxicity in Alzheimer’s disease (AD) and frontotemporal dementia (FTLD-tau). Previously, we found that pathogenic FTLD tau mutant (P301L) expression promotes aberrant trapping of Fyn in nanoclusters within hippocampal dendrites via an unknown mechanism (Padmanabhan et al., 2019). Here, we imaged Fyn-mEos2 using single particle tracking photoactivated localization microscopy (sptPALM) to demonstrate that nanoclustering of Fyn in hippocampal dendrites is promoted by Fyn’s open, primed conformation. Disrupting the auto-inhibitory, closed conformation of Fyn through phospho-inhibition, and perturbation of Fyn’s SH3 domain increases, Fyn’s nanoscale trapping. However, inhibition of Fyn’s catalytic domain has no impact on its mobility. Tau-P301L promotes Fyn lateral trapping via Fyn opening and ensuing increased catalytic activation. Pathogenic tau may therefore drive synaptotoxicity by locking Fyn in an open, catalytically active conformation, leading to postsynaptic entrapment and aberrant signalling cascades.
Impact of chronic transcranial Random-Noise Stimulation (tRNS) on prefrontal cortex excitation-inhibition balance in juvenile mice
Authors: Sánchez-León Carlos A. , Sánchez-López Álvaro , Gómez-Climent María A. , Cordones Isabel , Kadosh Roi Cohen , Márquez-Ruiz Javier
Published: September 2020

Transcranial random noise stimulation (tRNS), a non-invasive neuromodulatory technique capable of altering cortical activity, has been proposed to improve the signal-to-noise ratio at the neuronal level and the sensitivity of the neurons following an inverted U-function. The aim of this study was to examine the effects of tRNS on vGLUT1 and GAD 65-67 and its safety in terms of pathological changes. For that, juvenile mice were randomly distributed in three different groups: “tRNS 1x” receiving tRNS at the density current used in humans (0.3 A/m2, 20 min), “tRNS 100x” receiving tRNS at two orders of magnitude higher (30.0 A/m2, 20 min) and “sham” (0.3 A/m2, 15 s). Nine tRNS sessions during five weeks were administered to the prefrontal cortex of alert animals. No detectable tissue macroscopic lesions were observed after tRNS sessions. Post-stimulation immunohistochemical analysis of GAD 65-67 and vGLUT1 immunoreactivity showed a reduced GAD 65-67 immunoreactivity levels in the region directly beneath the electrode for tRNS 1x group with no significant effects in the tRNS 100x nor sham group. The observed results points to an excitatory effect associated with a decrease in GABA levels in absence of major histopathological alterations providing a novel mechanistic explanation for tRNS effects.
The Pleistocene species pump past its prime: evidence from European butterfly sister species
Authors: Ebdon Sam , Laetsch Dominik R. , Dapporto Leonardo , Hayward Alexander , Ritchie Michael G. , Dincă Vlad , Vila Roger , Lohse Konrad
Published: September 2020

The Pleistocene glacial cycles had a profound impact on the ranges and genetic make-up of organisms. Whilst it is clear that the contact zones that have been described for many sister taxa are secondary and have formed during the last interglacial, it is unclear when the taxa involved began to diverge. Previous estimates based on small numbers of loci are unreliable given the stochasticity of genetic drift and the contrasting effects of incomplete lineage sorting and gene flow on gene divergence. Here we use genome-wide transcriptome data to estimate divergence for 18 sister species pairs of European butterflies showing either sympatric or contact zone distributions. We find that in most cases species divergence predates the mid-Pleistocene transition or even the entire Pleistocene period. We also show that although post divergence gene flow is restricted to contact zone pairs, they are not systematically younger than sympatric pairs. This suggests that contact zones are not limited to the embryonic stages of the speciation process, but can involve notably old taxa. Finally, we show that mitochondrial and nuclear divergence are only weakly correlated and mitochondrial divergence is higher for contact-zone pairs. This suggests a possible role of selective sweeps affecting mitochondrial variation in maintaining contact zones.

Impact Summary

The influence of the Pleistocene glacial cycles on structuring species and genetic diversity in temperate taxa has permeated biogeographic and phylogeographic thinking for decades. Although phylogeographic studies have repeatedly claimed that the Pleistocene acted as a species pump, systematic tests of this idea based on robust estimates of species divergence are lacking. Here we estimate divergence times for all sister species pairs of European butterfly using genome-wide transcriptome data. We find that most species pairs are substantially older than the onset of Pleistocene glacial cycling. We also show that post divergence gene flow is restricted to pairs that form contact-zones. However, in contrast to expectations under a null model of allopatric speciation contract zone pairs are not necessarily younger than sympatric pairs.
The effect of response biases on resolution thresholds of Sloan letters in central and paracentral vision
Authors: Barhoom Hatem , Joshi Mahesh R , Schmidtmann Gunnar
Published: September 2020

Purpose

Letter resolution depends on three factors: perceivability, response bias, and similarity. The aim of the present study was to investigate the effect of response bias (the sensory-independent factor) on resolution thresholds of Sloan letters in central and paracentral vision.

Methods

Nine subjects with normal ocular health were recruited for this study. Using the method of constant stimuli, individual Sloan letters resolution thresholds were measured at 0° (central) and at ±3° eccentricity along the vertical meridian of the visual field. Response biases and letter similarities were computed using Luce’s choice model.

Results

Results showed that the differences in resolution thresholds of individual Sloan letters were significant at the central (F (9, 80) =5.02,p<.001), the upper (χ2 (9) = 50.38,p<.05) and the lower (χ2 (9) = 56.32,p<.05) visual field locations. Unlike letter similarity measures, response biases showed significant correlations to the differences in thresholds at the central (r = −0.83,p<.05), the upper (r = - 0.73,p<.05) and the lower (r = −0.70,p<.05) visual field locations.

Conclusions

Our findings suggest that response biases have a significant effect on resolution of Sloan letters that could result in overestimating resolution acuity in central and paracentral visual field locations.
Reduction of a Stochastic Model of Gene Expression: Lagrangian Dynamics Gives Access to Basins of Attraction as Cell Types and Metastabilty
Authors: Ventre Elias , Espinasse Thibault , Bréhier Charles-Edouard , Calvez Vincent , Lepoutre Thomas , Gandrillon Olivier
Published: September 2020

Differentiation is the process whereby a cell acquires a specific phenotype, by differential gene expression as a function of time. This is thought to result from the dynamical functioning of an underlying Gene Regulatory Network (GRN). The precise path from the stochastic GRN behavior to the resulting cell state is still an open question. In this work we propose to reduce a stochastic model of gene expression, where a cell is represented by a vector in a continuous space of gene expression, to a discrete coarse-grained model on a limited number of cell types. We develop analytical results and numerical tools to perform this reduction for a specific model characterizing the evolution of a cell by a system of piecewise deterministic Markov processes (PDMP). Solving a spectral problem, we find the explicit variational form of the rate function associated to a large deviations principle, for any number of genes. The resulting Lagrangian dynamics allows us to define a deterministic limit of which the basins of attraction can be identified to cellular types. In this context the quasipotential, describing the transitions between these basins in the weak noise limit, can be defined as the unique solution of an Hamilton-Jacobi equation under a particular constraint. We develop a numerical method for approximating the coarse-grained model parameters, and show its accuracy for a symmetric toggle-switch network. We deduce from the reduced model an approximation of the stationary distribution of the PDMP system, which appears as a Beta mixture. Altogether those results establish a rigorous frame for connecting GRN behavior to the resulting cellular behavior, including the calculation of the probability of jumps between cell types.
Aging selectively dampens oscillation of lipid abundance in white and brown adipose tissue
Authors: Held Ntsiki M. , Buijink M. Renate , Elfrink Hyung L. , Kooijman Sander , Janssens Georges E. , Vaz Frédéric M. , Michel Stephan , Houtkooper Riekelt H. , van Weeghel Michel
Published: September 2020

Lipid metabolism is under the control of the circadian system and circadian dysregulation has been linked to obesity and dyslipidemia. These factors and outcomes have also been associated to, or affected by, the process of aging. Here, we investigated whether murine white (WAT) and brown (BAT) adipose tissue lipids exhibit rhythmicity and if this is affected by aging. To this end, we have measured the 24 hour lipid profiles of WAT and BAT using a global lipidomics analysis of >1100 lipids. We observed rhythmicity in nearly all lipid classes including glycerolipids, glycerophospholipids, sterol lipids and sphingolipids. Overall, ~22% of the analyzed lipids were considered rhythmic in WAT and BAT. Despite a general accumulation of lipids upon aging the fraction of oscillating lipids decreased in both tissues to 14% and 18%, respectively. Diurnal profiles of lipids in BAT appeared to depend on the lipid acyl chain length and this specific regulation was lost in aged mice. Our study revealed how aging affects the rhythmicity of lipid metabolism and could contribute to the quest for targets that improve diurnal lipid homeostasis to maintain cardiometabolic health during aging.
Infra Red Thermography Reveals Transpirational Cooling in Pearl Millet (Pennisetum glaucum) Plants Under Heat Stress
Authors: Shanker Arun K. , Bhanu Divya , Sarkar Basudev , Yadav S.K. , Jyothilakshmi N. , Maheswari M.
Published: September 2020

An infra red thermographic analysis of well watered control and well watered heat stressed pearl millet (Pennisetum glaucum) was conducted at ICAR – Central Research Institute for Dryland Agriculture as a part of high resolution phenomics studies to identify the individual quantitative physiological parameters by plant phenotyping that form the basis for more complex abiotic stress tolerant traits. It was seen that the temperature gradient increased gradually from ground level to the top in the control non heat stressed plant. In contrast, it was seen that in the heat stressed plant the temperature increased up to the middle of the plant and then started to decrease at the top of the plant in comparison with the non heat stressed control plant. Our results indicate that the lowering of temperatures in the top of the heat stressed plant may be a mechanism by which the heat stressed plant acclimates to stress by regulating its transpiration thereby bringing in a cooling effect to counter stress.
Relationship of taxonomic error to frequency of observation
Authors: Stribling James B. , Leppo Erik W.
Published: September 2020

Biological nomenclature is the entry point to a wealth of information related to or associated with living entities. When applied accurately and consistently, communication between and among researchers and investigators is enhanced, leading to advancements in understanding and progress in research programs. Based on freshwater benthic macroinvertebrate taxonomic identifications, inter-laboratory comparisons of >900 samples taken from rivers, streams, and lakes across the U.S., including the Great Lakes, provided data on taxon-specific error rates. Using the error rates in combination with frequency of observation (FREQ; as a surrogate for rarity), six uncertainty/frequency classes (UFC) are proposed for approximately 1,000 taxa. The UFC, error rates, FREQ each are potentially useful for additional analyses related to interpreting biological assessment results and/or stressor response relationships, as weighting factors for various aspects of ecological condition or biodiversity analyses and helping set direction for taxonomic research and refining identification tools.
Cis-Regulatory Differences Explaining Evolved Levels of Endometrial Invasibility in Eutherian Mammals
Authors: Suhail Yasir , Maziarz Jamie D. , Dighe Anasuya , Wagner Gunter , Kshitiz
Published: September 2020

Eutherian (placental) mammals exhibit great differences in the degree of placental invasion into the maternal endometrium, with humans being on the most invasive end. Previously, we have shown that these differences in invasiveness is largely controlled by the stromal fibroblasts of the maternal endometrium, with secondary effect on stroma of other tissues resulting in correlated differences in cancer malignancy. Here, we present a statistical investigation of the second dogma linking the phenotypic and transcriptional differences to the genomic changes across species, revealing the regulatory genomic sequence differences underlying these inter-species differences. We show that gain or loss of specific transcription factor binding site sequences are connected to the inter-species gene-expression differences in a statistically significant manner, with a particularly larger effect on stromal genes related to invasibility. We also uncover transcriptional factors differentially regulating genes related to pro- and anti- invasible property of stroma. This work extends the understanding of inter-species differences in stromal invasion to the causal genomic sequence differences paving new avenues to target stromal characteristics to regulate placental, or cancer invasion.