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opencc-zeroOct 2020View details →

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during, and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Patterns of differentiation across nuclear genomes highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin.

opencc-zeroSep 2020View details →

Data from: Crop pollination services: complementary resource use by social vs solitary bees facing crops with contrasting flower supply

1. Many farmers are facing high economic risks if pollinator declines continue or temporal and spatial variation in wild bee communities cause reduced pollination services. Co-flowering crops might compete for pollinators, while they also might facilitate the delivery of pollination services. This rarely studied topic is of particular interest with respect to the foraging decisions of bees from different functional groups and when more sparsely and mass-flowering crops are in bloom at the same time. 2. The abundance of honey bees, bumble bees and solitary bees in strawberry fields was quantified with transect walks along a gradient of oilseed rape (OSR) availability (product of OSR land cover and temporally changing OSR flower cover). We established a pollination experiment with pollination treatments (open-, wind- and self-pollination) to study the effects of insect pollination on strawberry fruit weight and quality. 3. Changes in OSR availability exhibited contrasting effects on social versus solitary bees in strawberry fields. Bumble bees and honey bees were less abundant in strawberry fields when OSR availability was high, whereas solitary bees were facilitated. With more strawberry flowers we found more bees in general. 4. When flowers were open-pollinated they resulted in heavier fruits with better commercial grades compared to wind-and self-pollinated flowers. A higher bee abundance enhanced the strawberry fruit weight and quality but depended on flower order and variety. 5. Synthesis and applications. Sparsely flowering crops may compete with mass-flowering crops for social bee pollinators while solitary pollinators in the field might be even facilitated. To ensure best fruit weight and quality it can be beneficial to support bee abundance in the field. While some social and solitary bee species can be managed for pollination services, wild bees, in particular solitary species, should be conserved and promoted for stable crop pollination services in dynamic agricultural landscapes.

opencc-zeroOct 2020View details →

Genetic structuring in Atlantic haddock contrasts with current management regimes

<div class="WordSection1"> The advent of novel genetic methods has made it possible to investigate population structure and connectivity in mobile marine fish species: knowledge of which is essential to ensure a sustainable fishery. Haddock (Melanogrammus aeglefinus) is a highly exploited marine teleost distributed along the coast and continental shelf on both sides of the North Atlantic Ocean. However, little is known about its population structure. Here, we present the first study using single nucleotide polymorphism markers to assess the genetic population structure of haddock at multiple geographic scales, from the transatlantic to the local (fjord) level. Genotyping 138 SNP loci in 1329 individuals from 19 locations across the North Atlantic revealed three main genetic clusters, consisting of a Northwest Atlantic-, a Northeast Arctic- and a Northeast Atlantic cluster. We also observed a genetically distinct fjord population and a pattern of isolation-by-distance in the Northeast Atlantic. Our results contrast with the current management regime for this species in the Northeast Atlantic, as we found structure within some management areas. The study adds to the growing recognition of population structuring in marine organisms in general, and fishes in particular, and is of clear relevance for management of haddock in the Northeast Atlantic. </div>

opencc-by-4.0Aug 2020View details →

Expanded response data from Perrin et al. - Contrasts in Public Perception of the Role of Alien Species in Climate Driven Species Turnover

Responses given by 30 respondents from 3 different interest groups on their attitudes to climate change driven species turnover in Norwegian freshwater lakes. The groups are a) recreational fishers, b) individuals responsible for management decisions regarding freshwater lakes or rivers and c) academics involved in research regarding freshwater lakes or rivers. Use of square brackets indicates details have been altered so as to preserve anonymity of respondents. A total of 30 interviews were conducted between August of 2019 and April of 2020. Interviews lasted anywhere from 10 to 50 minutes. Of the 30 interviews, 16 were conducted in person, with the remaining 14 conducted via web meeting. Interview respondents were chosen using the snowball method, as described by Miles and Huberman <a href="https://paperpile.com/c/6PEtIR/dSUU/?noauthor=1">(1994)</a>. This requires an initial pool of contacts, who subsequently nominate other respondents that are suitable for the study.  In compliance with requirements of the Norwegian National Research Ethics Committee, all respondents were given an overview of the topic beforehand, assured that their responses would be anonymous, and informed of the intended use of their responses. All interviews were anonymously recorded and subsequently transcribed verbatim. Any details which might have allowed the individuals to be identified based on descriptions of their roles or locations were removed. As interviews were anonymous, ethics approval from the Norwegian National Research Ethics Committee was not required.

opencc-zeroNov 2020View details →

Contrasting effects of Miocene and Anthropocene levels of atmospheric CO2 on silicon accumulation in a model grass

Grasses are hyper-accumulators of silicon (Si) which they acquire from the soil and deposit in tissues to resist environmental stresses. Moreover, given the high metabolic costs of herbivore defensive chemicals and structural constituents (e.g. cellulose), grasses may substitute Si for these components when carbon (C) is limited. Indeed, high Si uptake grasses evolved in the Miocene when atmospheric CO2 concentration was much lower than present levels. It is; however, unknown how pre-industrial CO2 concentrations affect Si accumulation in grasses. Using Brachypodium distachyon, we hydroponically manipulated Si-supply (0.0, 0.5, 1, 1.5, 2 mM) and grew plants under Miocene (200 ppm) and Anthropocene levels of CO2 comprising ambient (410 ppm) and elevated (640 ppm) CO2 concentrations. We showed that regardless of Si-treatments, the Miocene CO2 levels increased foliar Si concentrations by 47% and 56% relative to plants grown under ambient and elevated CO2, respectively. This is due to higher accumulation overall, but also the reallocation of Si from the roots into the shoots. Our results suggest that grasses may accumulate high Si concentrations in foliage when carbon is less available (i.e. pre-industrial CO2 levels) but this is likely to decline under future climate change scenarios, potentially leaving grasses more susceptible to environmental stresses

opencc-by-4.0Dec 2020View details →

Deep Brain Image Contrast Classification

Deep Brain Image Contrast Classification

opencc-by-4.0Dec 2020View details →

Deep Brain Image Contrast Classification

Deep Brain Image Contrast Classification

opencc-zeroApr 2020View details →

Contrasting responses of different functional groups stabilise community responses to a dominant shrub under global change

1. Changes in precipitation regimes and nitrogen deposition levels due to global change are altering terrestrial ecosystems worldwide. Most attempts at understanding how biotic interactions affect plant species and community responses to global change have focused on biotic interactions measured at the community-level. However, these approaches ignore that communities include functionally dissimilar species that might respond differently to changes in the effects of dominant neighbours along environmental gradients. We test the hypothesis that plant species with differences in functional traits may exhibit contrasting interactions with a dominant shrub species within a single community, thereby stabilizing community-level responses to the effects of global change. 2. We manipulated water and nitrogen applications in a semi-arid dune community in northern China, quantified the biomass of herbaceous species occurring below the dominant shrub, Artemisia ordosica, and in adjacent open patches (without the shrub), and measured herbaceous species height and leaf dry matter content. The effects of A. ordosica were quantified at the species, group, and community levels using the relative interaction index (RII). Redundancy analysis was performed on species traits and the RII values to assess the relationships between functional differences in species and plant-plant interactions. Species were then grouped using a cluster analysis and the RII values were recalculated at the group level. 3. The redundancy analysis showed that species height and leaf dry matter content were significantly correlated to the changes in species' responses to the effect of A. ordosica along treatments. The four groups of species identified by the cluster analysis showed contrasting variations in competitive or facilitative responses depending on species traits and environmental treatments. However, the interactions measured at the group level balanced the community-level responses, as we found no significant changes in the effects of A. ordosica along treatments for community biomass, richness, and functional diversity indices. 4. Synthesis. Our findings indicate that species with different functional strategies within a community exhibit contrasting responses to a dominant shrub along environmental gradients. These contrasting changes in plant-plant interactions of functionally different species may balance the responses of community-level metrics. This suggests that functional differences between species groups and the balance of plant-plant interactions stabilize community responses to global change.

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-8 week

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-6 week

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-control group

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-4 week

Secondary formation of aerosols under typical high-humidity conditions in wintertime Sichuan Basin, China: A contrast to the North China Plain

The Sichuan Basin is one of the regions suffering from severe haze pollution in southwest China. However, the secondary aerosol formation in this region is poorly understood. In this study, the chemical compositions of PM2.5 and molecular compositions of water-soluble organics in wintertime Sichuan were measured to investigate the aerosol sources and formation under typical high relative humidity (RH) conditions. Strong correlations between PM2.5, carbonaceous aerosols and K+ suggested obvious influence of biomass burning. The impacts of biomass burning were also supported by the dominance of primarily emitted reduced/less oxidized nitrogen-containing organics as well as the high peak intensities of secondarily formed nitrocatechols and methyl-nitrocatechols. High humidity (average RH=80%) and aerosol liquid water (ALW) in Sichuan obviously facilitated the secondary formation of sulfate, nitrate and secondary organic aerosols (SOA). The average sulfate oxidation ratio and nitrogen oxidation ratio in Sichuan were 2.5 and 3.1 times of those in winter Beijing (average RH= 27%). This suggested higher potentials of SO2 and NOx to form sulfate and nitrate under high-RH conditions. The abundant aqueous-SOA formation in Sichuan was supported by the dominance of organosulfates (OSs) and nitrooxy-OSs in mass spectra of water-soluble organics, while the OSs in winter Beijing were quite limited. The more abundant OS formation in Sichuan was attributed to the much higher RH, ALW, aerosol acidity and sulfate, which favored the acidic sulfate-catalyzed aqueous-phase reactions for OS formation. Higher concentrations of biogenic volatile organic compounds were additional reasons for the more abundant OSs in Sichuan than in Beijing.

opencc-zeroJan 2021View details →

Contrasting patterns of sexually selected traits in Mediterranean and continental populations of European mouflon

The expression of sexually selected traits in highly dimorphic ungulates may be influenced by environmental quality. Variations in habitat conditions can impose different constraints on the allocation of energy resources to male life-history traits, and possibly alter the female preferences for specific features. Here, we compared the horn growth patterns in male European mouflon Ovis aries musimon living in different habitats (Mediterranean vs. continental) but sharing a common genetic origin. We hypothesized that the expression of sexually selected traits such as horn development should be promoted in more favourable habitat conditions (i.e., Mediterranean). Using linear mixed models on data retrieved from individuals harvested under the same hunting regime, we found longer horns and greater individual variance in horn segment length in the Mediterranean population than in the continental one. Furthermore, Mediterranean rams showed no evidence of compensatory horn growth, as opposed to the continental rams. Unexpectedly, horn base circumference was greater in the continental habitat than in the Mediterranean one. The overall results suggest different patterns of investment in horns in the two populations, with seemingly stronger pressure and consequences of sexual selection on mouflon rams living in more favourable environments. Although the role of hunters' selectivity cannot be excluded a priori, our data suggest that the differences in the expression of sexually selected traits in our study populations may be influenced by environmental conditions. Because sexual selection can impose substantial fitness costs on individuals, further investigations on the trade-offs between reproduction and survival would improve our understanding of the dynamics of mouflon populations living in different environmental conditions.

opencc-zeroJan 2021View details →

Contrasting fungal responses to wildfire across different ecosystem types

We took topsoil samples in burned and unburned areas across two California ecosystem types (Sonoma, California, United States) with differing fire ecologies in the immediate aftermath of a damaging wildfire in 2017. From our soil samples, we extracted DNA, amplified and sequenced fungal communities, and also measured chemistry (C%, N% and pH). Soil fungal communities of fire‐dependent oak woodlands differ from those of neighbouring mixed evergreen forests. The latter are more strongly altered compositionally by fire than the former. This repository contains code to run the analyses we presented in the associated paper (doi: 10.1111/mec.15767), as well as a phyloseq object with the molecular data and a few CSVs with the sample metadata.

opencc-zeroDec 2013View details →

Data from: Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics

Selective logging in Brazil allows for the removal of up to 90% of trees above 50 cm diameter of a given timber species, independent of a species' life history characteristics or how quickly it will recover. The genetic and demographic effects of selective logging on two Amazonian timber species (Dipteryx odorata Leguminosae, Jacaranda copaia Bignoniaceae) with contrasting ecological and reproductive characteristics were assessed in the same forest. Genetic diversity and gene flow were characterized by genotyping adults and seed sampled before and after logging, using hypervariable microsatellite markers. Overall, there were no short term genetic impacts on the J. copaia population, with commercial application of current Brazilian forest management regulations. In contrast, for D. odorata selective logging showed a range of genetic impacts, with a 10% loss of alleles, and reductions in siring by pollen from trees within the 546 ha study area (23% to 11%) and in the number of pollen donors per progeny array (2.8 to 1.6), illustrating the importance of the surrounding landscape. Asynchrony in flowering between D. odorata trees led to trees with no breeding partners, which could limit the species reproduction and regeneration under current regulations. The results are summarised with other published studies from the same site and the implications for forest management discussed. The different types and levels of impacts associated with each species support the idea that ecological and genetic information by species, ecological guild or reproductive group are essential in helping to derive sustainable logging guidelines for tropical forests.

opencc-zeroDec 2017View details →

Data from: Contrasting patterns of population history and seed-mediated gene flow in two endemic Costa Rican oak species

Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in two partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. Phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.

opencc-zeroDec 2012View details →

Data from: Contrasting genetic responses to population fragmentation in a coevolving fig and fig wasp across a mainland-island archipelago

Interacting species of pollinator–host systems, especially the obligate ones, are sensitive to habitat fragmentation, due to the nature of mutual dependence. Comparative studies of genetic structure can provide insights into how habitat fragmentation contributes to patterns of genetic divergence among populations of the interacting species. In this study, we used microsatellites to analyse genetic variation in Chinese populations of a typical mutualistic system – Ficus pumila and its obligate pollinator Wiebesia sp. 1 – in a naturally fragmented landscape. The plants and wasps showed discordant patterns of genetic variation and geographical divergence. There was no significant positive relationship in genetic diversity between the two species. Significant isolation-by-distance (IBD) patterns occurred across the populations of F. pumila and Wiebesia sp. 1 as whole, and IBD also occurred among island populations of the wasps, but not the plants. However, there was no significant positive relationship in genetic differentiation between them. The pollinator populations had significantly lower genetic variation in small habitat patches than in larger patches, and three island pollinator populations showed evidence of a recent bottleneck event. No effects of patch size or genetic bottlenecks were evident in the plant populations. Collectively, the results indicate that, in more fragmented habitats, the pollinators, but not the plants, have experienced reduced genetic variation. The contrasting patterns have multiple potential causes, including differences in longevity and hence number of generations experiencing fragmentation; different dispersal patterns, with the host's genes dispersed as seeds as well as a result of pollen dispersal via the pollinator; asymmetrical responses to fluctuations in partner populations; and co-existence of a rare second pollinating wasp on some islands. These results indicate that strongly interdependent species may respond in markedly different ways to habitat fragmentation.

opencc-zeroNov 2019View details →

Data from: Contrasting global patterns of spatially periodic fairy circles and regular insect nests in drylands

Numerical analysis of spatial pattern is widely used in ecology to describe the characteristics of floral and faunal distributions. These methods allow attribution of pattern to causal mechanisms by uncovering the specific signatures of patterns and causal agents. For example, grassland‐gap patterns called fairy circles (FCs) in Namibia and Australia are characterized by highly regular and homogenous distributions across landscapes that show spatially periodic ordering. These FCs have been suggested to be caused by both social insects and competitive plant interactions. We compared eight Namibian and Australian FC patterns and also modeled FCs to 16 patterns of social insect nests in Africa, Australia, and America that include the most regular termite mound patterns known. For pattern‐process inference, we used spatial statistics based on both nearest‐neighbor analysis and neighborhood‐density functions. None of the analyzed insect‐nest distributions attain the spatially periodic ordering that is typical of FCs. The inherently more variable patterns of termite and ant nests are commonly attributable to well documented aspects of the faunal life‐history. Our quantitative evidence from drylands shows that the more variable insect‐nest distributions in water‐limited environments cannot explain the characteristic spatial signature of FCs. The analysis demonstrates the interpretation of scale‐dependent neighborhood‐density functions and that it is the identification of unique spatial signatures in regular patterns that need to be linked to process. While our results cannot verify a specific hypothesis, they support the hypothesis that FCs in these drylands are more likely an emergent vegetation pattern caused by strong plant competition for water.