Find research datasets worth reusing

The diversity of mycorrhiza-associated fungi and trees shape subtropical mountain forest ecosystem functioning

Aim: Mycorrhiza play key roles in ecosystem structure and functioning in forests. However, how different mycorrhizal types influence mountain forest biodiversity-ecosystem functioning relationships is largely unknown. We evaluate how the diversity of distinct mycorrhiza-associated fungi and trees shape forest carbon storage along elevational gradients. Location: Gaoligong Mountains within Hengduan Mountains, Southwest China. Taxon: Seed plants and mycorrhizal fungi. Methods: We used the data from 31 subtropical forest plots along elevational gradients on two aspects (east and west) of the mountain. We quantified species richness of trees and symbiotic fungi and assigned both to their mycorrhizal type (arbuscular mycorrhiza (AM), ectomycorrhiza (EcM) and ericoid mycorrhiza (ErM)). We then examined the diversity effects of mycorrhiza-associated fungi and trees on above-ground carbon stored in trees and organic carbon stored in soils. Results: Species richness was highest for AM trees (79.5%), followed by ErM trees (13.4%) and then EcM trees (7.1%). Species richness of AM-associated trees and fungi decreased with increasing elevation, while ErM-associated trees and fungi showed an opposite trend. EcM-associated diversity followed a hump-shaped relationship with elevation. Positive relationships between diversity and above-ground carbon were detected in all three mycorrhizal associations, but despite low species number, canopy-dominating EcM trees comprised 64.4% of the amount of above-ground carbon. Furthermore, community-weighted means of height exhibited positive correlations with forest above-ground carbon, indicating that positive selection effects occur. Soil organic carbon was positively related to EcM-associated fungi diversity, above-ground carbon mass and soil nitrogen availability, with the latter having the strongest direct effects. Main conclusions: The distributions of forest biodiversity and carbon storage can be modulated by distinct mycorrhizal fungi and trees. Moreover, future global changes (e.g., climate warming, intensifying nitrogen deposition) could alter the mycorrhizal-mediated biodiversity-ecosystem functioning relationships in mountain forests.

Activity in developing prefrontal cortex is shaped by sleep and sensory experience

In developing rats, behavioral state exerts a profound modulatory influence on neural activity throughout the sensorimotor system, including primary motor cortex (M1). We hypothesized that similar state-dependent modulation occurs in prefrontal cortical areas with which M1 forms functional connections. Here, using 8- and 12-day-old rats cycling freely between sleep and wake, we record neural activity in M1, secondary motor cortex (M2), and medial prefrontal cortex (mPFC). At both ages in all three areas, neural activity increased during active sleep (AS) compared with wake. Also, regardless of behavioral state, neural activity in all three areas increased during periods when limbs were moving. The movement-related activity in M2 and mPFC, like that in M1, is driven by sensory feedback. Our results, which diverge from those of previous studies using anesthetized pups, demonstrate that AS-dependent modulation and sensory responsivity extend to prefrontal cortex. These findings expand the range of possible factors shaping the activity-dependent development of higher-order cortical areas.

Bumblebees' food preferences are jointly shaped by rapid valuation of nectar sugar concentration and viscosity

Animals are often assumed to follow a strategy of energy maximisation, and therefore should evaluate feeding options based on energy intake rates. Contrastingly, rhesus macaque's learned food preferences are based on sensory properties, e.g. sweetness and resistance, regardless of energy differences. Here, we show that nectar sugar concentration (sweetness) and nectar viscosity (resistance) drive preferences of bumblebees, classical models for economic and foraging decision-making. Using a tasteless/odourless biopolymer (tylose), we created feeding options that differed in sweetness and resistance, properties that affect energy intake rate and can be immediately sensed. When energy intake rates were similar, bumblebees developed preferences based on sweetness and resistance. When energy intake rates were different but sweetness and resistance were balanced against each other, bees developed no preferences. Decision dynamics during training indicated that bumblebees simultaneously evaluated sweetness and resistance to make decisions quickly (in seconds). These results indicate that bumblebees' food preferences are jointly affected by the immediate sensation of nectar sweetness and resistance as positively and negatively reinforcing properties, respectively, irrespective of energy intake rate. From these findings we propose that subjective valuations of sensory food properties should be considered as constraints in models of foraging behaviour.

Simultaneous integration and modularity underlie the exceptional body shape diversification of characiform fishes

Evolutionary biology has long striven to understand why some lineages diversify exceptionally while others do not. Most studies have focused on how extrinsic factors can promote differences in diversification dynamics, but a clade's intrinsic modularity and integration can also catalyze or restrict its evolution. Here, we integrate geometric morphometrics, phylogenetic comparative methods and visualizations of covariance to infer the presence of distinct modules in the body plan of Characiformes, an ecomorphologically diverse fish radiation. Strong covariances reveal a cranial module, and more subtle patterns support a statistically significant subdivision of the postcranium into anterior (precaudal) and posterior (caudal) modules. We uncover substantial covariation among cranial and postcranial landmarks, indicating body-wide evolutionary integration as lineages transition between compressiform and fusiform body shapes. A novel method of matrix subdivision reveals that within- and among-module covariation contributes substantially to the overall eigenstructure of characiform morphospace, and that both phenomena led to biologically important divergence among characiform lineages. Functional integration between the cranium and post-cranial skeleton appears to have allowed lineages to optimize the aspect ratio of their bodies for locomotion, while the capacity for independent change in the head, body and tail likely eased adaptation to diverse dietary and hydrological regimes. These results reinforce a growing consensus that modularity and integration synergize to promote diversification.

opencc-by-4.0Jan 2023View details →

raw and processed X-ray scattering datasets for: "Entering a New Dimension in Powder Processing for Advanced Ceramics Shaping"

This dataset is a complete set of raw, processed and analyzed data, associated with the manuscript mentioned in the title.  Data is stored in HDF5 containers following the NeXus structure definitions. Data is in absolute units, and with traceable scattering and intensity values following our "MOUSE" methodology, described in <a href="https://dx.doi.org/10.1088/1748-0221/16/06/P06034">10.1088/1748-0221/16/06/P06034</a> Data on the samples as well as backgrounds have been included as well as the processing sequence and -values. Data has been processed using the <a href="https://dx.doi.org/10.1107/S1600576717004708">DAWN software package</a>.  All associated metadata and processing history has been added. Particle size distribution analyses using McSAS are included as well.  The samples consisted of a 4.2 mass% dispersion of yttria-stabilized zirconia nanoparticles in a cross-linked matrix. The measurements show a good dispersion with minimal agglomeration. The wide-angle region shows diffraction information consistent with zirconia.

opencc-zeroJan 2023View details →

Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We used resequenced whole genomes to investigate how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpeckers, species co-distributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (1) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (2) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.

opencc-zeroJan 2023View details →

Climate and microhabitat shape the prevalence of endozoochory in the seed rain of tropical montane forests

Endozoochory, the dispersal of seeds by animal ingestion, is the most dominant mode of seed dispersal in tropical forests and is a key process shaping current and future forest dynamics. However, it remains largely unknown how endozoochory is associated with environmental conditions at regional and local scales. Here, we investigated the effects of elevation, climate and microhabitat conditions on the proportion of endozoochorous plant species in the seed rain of the tropical Andes of southern Ecuador. Over one year, we measured seed rain in 162 seed traps on nine 1-ha forest plots located at 1000 m, 2000 m, and 3000 m a.s.l. We recorded climatic conditions (mean annual temperature and rainfall) in each plot and microhabitat conditions (leaf area index and soil moisture) adjacent to each seed trap. In total, we recorded 331,838 seeds belonging to 323 morphospecies. Overall, the proportion of endozoochorous species in the seed rain decreased with elevation. Relative biomass of endozoochorous species decreased with increasing rainfall, whereas the relative seed richness of endozoochorous species increased with increasing temperature and leaf area index. These findings suggest an interplay between climate factors and microhabitat conditions in shaping the importance of endozoochorous plant species in the seed rain of tropical montane forests. We conclude that changing climatic and microhabitat conditions are likely to cause changes in the dominant dispersal modes of plant communities which may trigger changes in current and future dynamics of tropical forests.

opencc-zeroJan 2023View details →

Global expansion of a solitary-social tropical spitting spider shaped by multiple long-distance dispersals

The spitting spider Scytodes fusca is well known species complex for its unusual hunting technique which involves spitting a venomous sticky silken substance over its prey. Previous studies supposed that S. fusca was native to Central and Southern America but had been expanded to the tropics of almost every continent. We aimed to test the hypothesis of a Neotropical origin for this spider followed by a secondary dispersal to other regions, and to discuss how population expansion occurred in the tropics was driven. We investigated the population structure and spatiotemporal biogeography of the species complex through a culmination of a 22-year comprehensive global sampling using the mitochondrial and nuclear loci (COI, 16S, 18S, 28S, H3 and ITS2). The S. fusca species complex is divided into two clades. One clade comprises the haplotypes from Australasian regions and a haplotype from Baja Peninsula, Mexico. The other is composed of the haplotypes from all analyzed regions including Asia, Australia, the Americas and Madagascar. The Americas and Madagascar populations exhibit a lower genetic diversity compared with the Australasian population, and both have different population demographic histories. The initial divergence within the species complex started during the early Miocene. Diversifications of both clades occurred during the late Miocene. One haplotype was recently and widely dispersed into Southeast Asia, South Asia, Australia, the Americas and Madagascar. Our results elucidate the global spread history of the S. fusca species complex, suggesting a Malay Archipelago origin, two expansion routes, and its multiple dispersals into the Americas that stem from a common native source population, as well as from Australia, Fiji, French Polynesia, or Turks and Caicos bridgeheads. Our data support that the expansion of the S. fusca species complex from Australasia to America and Madagascar was facilitated by long-distance jump dispersal events.

opencc-byJan 2023View details →

Double-barreled enterostomy with delayed compression anastomosis by shape memory titanium nickelide device in children

The problem of children with enterostomy is still current, increase number of early and late complications of stoma formation and closure.The aim of the study is to improve the outcomes of surgical treatment of newborns and infants with double-barreled enterostomies using a shape memory titanium nickelide device and creating a delayed compression anastomosis.Materials and methods. The clinical part of the study included children aged 0 to 6 months with congenital or acquired intestinal pathology with the formation of various types of enterostomy. The study groups included children with Mikulicz double-barreled enterostomies and Bishop-Koop T-shaped anastomoses. In the experimental part of the study, compression and manual anastomoses with enterostomies were compared in laboratory models (rabbits).Expected results of the study. Compression anastomosis in a double-barreled enterostomy in newborns and infants is a safe and effective alternative to manual T-anastomosis, allows to reduce pathological loss of chyme and eliminate suture failure, close the stoma without resection in delayed period.

Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 1

Part one of the data used for the generation of the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.

Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 2

Part 2 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.

opencc-by-nc-4.0Feb 2023View details →

Theoretical prediction and shape-controlled synthesis of two-dimensional semiconductive Ni3TeO6

Check the reference: Fernández-Catalá, J.; Kistanov, A., A.; Bai, Y.; Singh, H.; Cao, W. npj 2D Mater. Appl. 2023, 7, 1, 48

Datasets and R script to replicate the theoretical modeling from the article entitled Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission

Datasets and R script to replicate the theoretical modeling from the article entitled " Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission" by Vantaux A., Moiroux N., Dabire K. R., Cohuet A., Lefevre T. 2023

opencc-zeroFeb 2023View details →

Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10–120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

Canopy height, rather than neighborhood effects, shapes leaf herbivory in a tropical rainforest

These files contain the datasets and R codes used in the data analyses in the paper " Canopy height, rather than neighborhood effects, shapes leaf herbivory in a tropical rainforest " that will be published in Ecology.

opencc-zeroFeb 2023View details →

Island area and remoteness shape plant and soil bacterial diversity through land use and biological invasion

Biodiversity is declining dramatically due to human-driven land use change and biological invasion, but our knowledge of how such drivers influence plant and heterotroph diversity on island ecosystems remains limited. Historically island biogeography theory has focused solely on the direct effects of island size and remoteness on biodiversity, but these factors can also indirectly affect species gain and/or loss by impacting land use change and biological invasion. We built the structural equation model to explore the direct effects of island size and remoteness, and indirect effects of these factors via land use intensity and pinewood nematode invasion, on the diversity of plants and soil bacteria across 37 continental shelf islands in the largest land-bridge archipelago in eastern China. As expected we found that increasing island area directly promoted plant diversity. However, land use intensity increased with island area which also promoted plant diversity, and loss of pine forest by the pinewood nematode invasion increased with island remoteness which reduced plant diversity. Island remoteness only indirectly reduced plant diversity through increasing pine forest loss. Soil bacterial diversity was directly negatively impacted by island remoteness, and indirectly negatively impacted by island remoteness through increased soil electrical conductivity likely caused by greater salinity from sea spray. Furthermore, soil bacterial diversity was indirectly promoted by island area through increased plant diversity and decreased soil electrical conductivity, and indirectly reduced by pine forest loss through decreased plant diversity. Our findings highlight that island biogeography theory has relevance to understanding human impacts in the Anthropocene, and that there is a need to more explicitly recognize how island size and remoteness affect biodiversity not only directly, but also indirectly via their effects on human-induced drivers of biodiversity, such as land use change and biological invasion.

openother-openDec 2022View details →

Global beta-diversity of angiosperm trees is shaped by Quaternary climate change

This release contains the code and data used in the paper: Wu-Bing Xu et al., Global beta-diversity of angiosperm trees is shaped by Quaternary climate change. Sci. Adv. 9, eadd8553 (2023). DOI: <a href="https://doi.org/10.1126/sciadv.add8553">10.1126/sciadv.add8553</a>

opencc-by-4.0Dec 2030View details →

Agta hunter-gatherer oral microbiomes are shaped by contact network structure

Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African Bayaka hunter-gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses, and even unrelated friends, can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

opencc-by-4.0Mar 2023View details →

Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom

In 2020 we sampled a complete spring bloom in the German Bight over a 90-day period. Bacterioplankton metagenomes from 30 time-points allowed reconstruction of 251 metagenome-assembled genomes (MAGs). Corresponding metatranscriptomes highlighted 50 particularly active MAGs of the most abundant clades. Saccharide measurements together with bacterial polysaccharide utilization loci (PUL) expression data identified β-glucans (diatom laminarin) and α-glucans as the most prominent dissolved polysaccharide substrates metabolized by the bacterioplankton. Here we are depositing all supporting environmental data for the analyzed  2020 Helgoland spring algal bloom. This includes physicochemical data, data on algal abundances and biovolumes, data on copepod and flagellate abundances, data on monosaccharide and antibody-based polysaccharide measurements, and 16S rRNA-based bacterial diversity data. The corresponding metagenome, metatranscriptome and MAG sequence data of this project are available from the European Nucleotide Archive (accession PRJEB52999).