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publicDec 2023View details →

Data for: A novel and enhanced calibration of the tilting weir as a flow measurement structure

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publicApr 2024View details →

Data from: Forestry impacts on stream flows and temperatures: A quantitative synthesis of paired catchment studies across the Pacific salmon range

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publicMay 2024View details →

Data from: Amazonian rivers are leaky barriers to gene flow in forest understory birds

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publicApr 2020View details →

Data from: The utility of information flow in formulating discharge forecast models: a case study from an arid snow-dominated catchment

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Water column dissolved (DSi) and biogenic (BSi) concentrations and fluxes collected from Sweeney (Right), West (Left) and Clubhead along with temperature, salinity, and flow data from 7/2010

Found at the landesea interface, these systems are silica replete with large stocks in plant biomass, sediments, and porewater, and therefore, have the potential to play a substantial role in the transformation and export of silica to coastal waters. In an effort to better understand this role, we measured the fluxes of dissolved (DSi) and biogenic (BSi) silica into and out of two tidal creeks in the PIE LTER salt marsh system. One of the creeks (Sweeney) has been fertilized from May to September for six years allowing us to examine the impacts of nutrient addition on silica dynamics within the marsh.

openCustomJan 2020View details →

opencc-by-4.0Aug 2019View details →

Subglacial Drainage Evolution Modulates Seasonal Ice Flow Variability of Three Tidewater Glaciers in Southwest Greenland - velocity and plume data

This file contains four datasets: - ice velocity estimates of the area surrounding and including Kangiata Nunata Sermia, southwest Greenland, derived from Landsat imagery and from Sentinel 1 imagery - plume observations in this area - subglacial discharge at the terminus - glacier terminus positions A more complete description of these datasets will be provided in the publication with the same name (currently in review). The methods used to measure glacier terminus positions are described in https://doi.org/10.5194/esurf-6-551-2018

opencc-by-4.0Jun 2020View details →

Simulation data and scripts for CFD-DEM simulation of granular flows in ambient fluid

<ul> <li>Data sets - contains the raw data required to replicate and validate all plots in the main article. Contains folders in containing measurements of basic flow properties, e.g. velocities, shear rates, etc., of monodisperse and bidisperse granular flows in different flow regimes. Each folder contains a ReadMe.txt briefly explaining the content and lay out of each data set.</li> <li>Sample case - a .zip file which includes codes which are needed to simulate a CFD-DEM case of a steady granular flow in water with cyclic boundaries in the stream wise direction. Also enclosed is a ReadMe.txt file detailing the implementation instructions for both Esys particle and OpenFOAM codes. Download links for Esys particle and OpenFOAM are also included.</li> <li>Geo file generator - a .zip file which includes Esys particle codes that can be used to generate a .geo file specifying the initial position of the particles used in the test simulations. A ReadMe.txt file is enclosed with more detailed implementation instructions.</li> </ul>

openother-ncJun 2020View details →

CellCognize: a neural network pipeline for cell type classification from flow cytometry data

Readme file content The files stored here contain the following material as supplementary and source data for the publication Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data Birge D. Özel Duygan1, Noushin Hadadi1, Ambrin Farizah Bab1, Markus Seyfried2, Jan R. van der Meer1 1 Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland 2 Biotechnology Department, Firmenich SA, Geneva, Switzerland %%%%%%% Flow cytometry data %%%%%% FCM_files: .mat files with cleaned data as described in the supplementary methods section Ecoli_lakewater: raw FCM data (in .csv format) of E. coli cultures and E. coli cultures mixed to lakewater MIX_experiment_ACL_AJH_PVR: raw FCM data (in .csv format) of the synthetic three culture experiment with E. coli, A. johnsonii and P. veronii, as described in the main text and SI methods. PHE_OCT_enrichments: raw FCM data (in .csv format) of the phenol and 1-octanol enrichments and the 1-octanol isolates, as described in the main text and SI methods. %%%%%%% Neural network data %%%%%% NN_file_example: three ANN functions, to be used in conjunction with the SI methods section Supplementary_Methods.docx: Detailed description on the construction, usage and scripts for the ANN. To be used in conjunction with the Flow Cytometry data %%%%%%% 16S sequencing data %%%%%% raw fastq- files of the sample reads of the 1-octanol and phenol enrichments described in the paper, at t=0 and t=3d, each in triplicates, forward and reverse. Readme_16S_sequence_files.txt: sample description of the read files

Data from: When does gene flow facilitate evolutionary rescue?

Experimental and theoretical studies have highlighted the impact of gene flow on the probability of evolutionary rescue in structured habitats. Mathematical modelling and simulations of evolutionary rescue in spatially or otherwise structured populations showed that intermediate migration rates can often maximize the probability of rescue in gradually or abruptly deteriorating habitats. These theoretical results corroborate the positive effect of gene flow on evolutionary rescue that has been identified in experimental yeast populations. The observations that gene flow can facilitate adaptation are in seeming conflict with traditional population genetics results that show that gene flow usually hampers (local) adaptation. Identifying conditions for when gene flow facilitates survival chances of populations rather than reducing them remains a key unresolved theoretical question. We here present a simple analytically tractable model for evolutionary rescue in a two-deme model with gene flow. Our main result is a simple condition for when migration facilitates evolutionary rescue, as opposed as no migration. We further investigate the roles of asymmetries in gene flow and / or carrying capacities, and the effects of density regulation and local growth rates on evolutionary rescue.

Data from: Quaternary land bridges have not been universal conduits of gene flow

Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel of five songbird species complexes covering a range of ecological specificities to investigate the effects Quaternary land bridges have had on the connectivity of Southeast Asian forest biota. Specifically, we combined morphological and bioacoustic analysis with an arsenal of population-genomic and modelling approaches applied to thousands of genome-wide DNA markers across a total of hundreds of individuals. Our analyses show that species dependent on forest understorey exhibit deep differentiation between Borneo and western Sundaland, with no evidence of gene flow during the land bridges accompanying the last 1-2 ice ages. In contrast, dispersive canopy species and habitat generalists have experienced more recent gene flow. Our results argue that there remains much cryptic species-level diversity to be discovered in Southeast Asia even in well-known animal groups such as birds, especially in non-dispersive forest understorey inhabitants. We also demonstrate that Quaternary land bridges have not been equally suitable conduits of gene flow for all species complexes, and that life history is a major factor in predicting relative population divergence time across Quaternary climate fluctuations.

Data from: Out of sight, out of mind: Widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal

Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting as a cause of intra- or inter-genomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both incomplete lineage sorting and introgression as a case for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both incomplete lineage sorting and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by incomplete lineage sorting, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that results from the plastid genome do not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought.

Data from: Persistent firing and adaptation in optic-flow-sensitive descending neurons

A general principle of sensory systems is that they adapt to prolonged stimulation by reducing their response over time. Indeed, in many visual systems, including higher-order motion sensitive neurons in the fly optic lobes and the mammalian visual cortex, a reduction in neural activity following prolonged stimulation occurs. In contrast to this phenomenon, the response of the motor system controlling flight maneuvers persists following the offset of visual motion. It has been suggested that this gap is caused by a lingering calcium signal in the output synapses of optic lobe neurons. However, whether this directly affects the responses of the post-synaptic descending neurons, leading to the observed behavioral output, is not known. We use extracellular electrophysiology to record from optic flow sensitive descending neurons in response to prolonged wide-field stimulation. We find that, as opposed to most sensory and visual neurons, and in particular to the motion vision sensitive neurons in the brains of flies and mammals, the descending neurons show little adaption during stimulus motion. In addition, we find that the optic flow sensitive descending neurons display persistent firing, or an after-effect, following the cessation of visual stimulation, consistent with the lingering calcium signal hypothesis. However, if the difference in after-effect is compensated for, subsequent presentation of stimuli in a test-adapt-test paradigm reveals adaptation to visual motion. Our results thus show a combination of adaptation and persistent firing, in the neurons that project to the thoracic ganglia, and thereby control behavioral output.

opencc-zeroAug 2020View details →

Data from: Gene flow at the leading range edge - the long-term consequences of isolation in European Beech (Fagus sylvatica L. Kuhn)

Aim: Isolation is expected to lead to negative impacts on populations due to a reduction in effective population size and gene flow, exacerbating the effects of genetic drift, which might be stronger in peripheral and fragmented populations. Fagus sylvatica (European beech) in southern Sweden presents a gradient of isolation towards the leading range edge of the species. We sought to determine the impact of long-term isolation on genetic diversity and population genetic structure within populations of this species. Location: Samples were obtained from 14 sites towards the northern edge of the native range of beech in Sweden. Taxon: Fagaceae Methods: Using historical sources, we obtained area- and distance-based measures of isolation. We measured genetic diversity and structure by using nuclear microsatellite marker data, and performed parentage analysis to estimate external pollen-mediated gene flow. We implemented a partial least squares regression to determine the effects of isolation on each of the genetic diversity estimators and the measures of external pollen-mediated gene flow. Results: Long-term isolation generally had a negative impact on genetic diversity, which is exacerbated over time, further affecting progeny and suggesting that isolated populations are subject to strong genetic drift, possibly due to the combination of founder events and persistent small population sizes. Bayesian cluster analysis revealed that isolation was also acting as a barrier to gene flow in the north-eastern distribution of beech. Main conclusions: Isolation at the leading range edge of beech in Sweden has created gradients of contemporary gene flow within the species. The long-term cumulative effects of isolation on this wind-pollinated tree species and its negative impacts on genetic diversity and gene flow, could lead to inbreeding depression and higher extinction risk where populations remain small and isolated.

opencc-zeroAug 2020View details →

Data from: Ocean warming and acidification alter the behavioural response to flow of the sea urchin Paracentrotus lividus

Ocean warming (OW) and acidification (OA) are intensively investigated as they pose major threats to marine organism. However, little effort is dedicated to another collateral climate change stressor, the increased frequency and intensity of storm events, here referred to as intensified hydrodynamics. A 2-month experiment was performed to identify how OW and OA (temperature: 21°C; pHT: 7.7, 7.4; control: 17°C-pHT7.9) affect the resistance to hydrodynamics in the sea urchin Paracentrotus lividus using an integrative approach that includes physiology, biomechanics and behaviour. Biomechanics was studied under both no-flow condition at the tube foot (TF) scale and flow condition at the individual scale. For the former, TF disk adhesive properties (attachment strength, tenacity) and TF stem mechanical properties (breaking force, extensibility, tensile strength, stiffness, toughness) were evaluated. For the latter, resistance to flow was addressed as the flow velocity at which individuals detached. Under near- and far-future OW and OA, individuals fully balanced their acid-base status, but skeletal growth was halved. TF adhesive properties were not affected by treatments. Compared to the control, mechanical properties were in general improved under pHT7.7 while in the extreme treatment (21°C-pHT7.4) breaking force was diminished. Three behavioural strategies were implemented by sea urchins and acted together to cope with flow: improving TF attachment, streamlining and escaping. Behavioural responses varied according to treatment and flow velocity. For instance, individuals at 21°C-pHT7.4 increased the density of attached TF at slow flows or, controlled TF detachment at fast flow to compensate for weakened TF mechanical properties. They also showed an absence of streamlining favouring an escaping behaviour as they ventured in a riskier faster movement at slow flows. At faster flows, the effects of OW and OA were detrimental causing earlier dislodgment. These plastic behaviours reflect a potential scope for acclimation in the field, where this species already experiences diel temperature and pH fluctuations.

opencc-zeroAug 2020View details →

Data from: Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype

Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident European brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) a positive effect of admixture with the closely related anadromous river lamprey (L. fluviatilis) ecotype on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled from 81 sites upstream and downstream barriers to migration, in 29 western European rivers. Linear modelling revealed a strong positive relationship between genetic diversity and the distance from the river source, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal mediated by water flow. Downstream L. planeri populations in sympatry with L. fluviatilis displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic make-up of upstream L. planeri populations whereas admixture between ecotypes maintains higher levels of genetic diversity in L. planeri populations sympatric with L. fluviatilis. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks.

opennotspecifiedSep 2020View details →

Figure 4 in Optimizing biodiversity informatics to improve information flow, data quality, and utility for science and society

Figure 4. Graphical representation of original and recently modified pathways for feedback regarding Primary Biodiversity Data, showing information transfer among users, providers, and aggregators. Such feedback consists of suggested improvements or additions to data fields, for example a change in species identification or a newly determined georeference. The diagrams contrast two complementary mechanisms: (a) the original feedback loop (currently dominant); and (b) the emerging feedback pendulum (proposed for expansion). In a: (1) the user sends feedback to the provider (e.g., a given natural history museum); (2) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (3) that information becomes available for query by all users. In practice, because many providers do not consistently make such changes (denoted by an X), users do have access to updated information (dashed line). In b: (1) the user sends feedback to the aggregator; (2) the aggregator simultaneously both annotates the record (visible to all users) and sends the suggested information to the provider; (3) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (4) the aggregator makes the updated information available for query by all users. Note that even if a provider takes no action regarding the suggested information, the annotations placed by the aggregator are nevertheless available to users. Additionally, because the quantifications of data quality and use described in the text allow for benchmarks that can be tracked over time, we anticipate that the feedback pendulum will help providers become more successful in justifying and securing funding to make data improvements based on feedback from users.

opencc-zeroOct 2020View details →

Data for the effect of optic flow cues on honeybee flight control in wind

To minimise the risk of colliding with the ground or other obstacles, flying animals need to control both their ground speed and ground height. This task is particularly challenging in wind, where head winds require an animal to increase its airspeed to maintain a constant ground speed and tail winds may generate negative airspeeds, rendering flight more difficult to control. In this study, we investigate how head and tail winds affect flight control in the honeybee Apis mellifera, which is known to rely on the pattern of visual motion generated across the eye – known as optic flow – to maintain constant ground speeds and heights. We find that, when provided with optic flow cues in both the longitudinal and transverse directions of flight, honeybees maintain a constant ground speed but fly lower in head winds and higher in tail winds, a response that is also observed when longitudinal optic flow cues are minimised. This change in height with wind does not appear to result in a constant rate of optic flow in the ventral visual field, suggesting that honeybees may rely on a combination of mechanosensory and visual information when controlling flight in wind. We also find that, when the transverse component of optic flow is minimised, or when all optic flow cues are minimised, the effect of wind on ground height is abolished. We propose that the regular sidewards oscillations that the bees make as they fly may be used to extract information about the distance to the ground, independently of the longitudinal optic flow that they use for ground speed control. This computationally simple strategy could have potential uses in the development of lightweight and robust systems for guiding autonomous flying vehicles in natural environments.

opencc-by-4.0Nov 2020View details →

Raw data for reference flow experiments

Raw results data for the reference flow study. Reference flow used public sequence data, where is specified in the manuscript, to generate the results. The figures shown in the manuscript were plotted using the provided processed data.   Reference flow manuscript: https://www.biorxiv.org/content/10.1101/2020.03.03.975219v4 Reference flow software: https://github.com/langmead-lab/reference_flow Software for reference flow experiments: https://github.com/langmead-lab/reference_flow-experiments An archived version of the software for experiments: https://doi.org/10.5281/zenodo.4287729

opencc-by-4.0Dec 2020View details →

Soil water retention and water flow simulation data

The data is for the manuscript of a paper entitled "Simulation of water flow and calculation of the related physical quality indices as influenced by soil water retention curve fitting methods". Accurate fitting of soil water retention curve (SWRC) parameters is crucial in the modeling of soil water flow and the assessment of soil quality. The un-weighted least squares regression (ULS) is the most common approach applied for fitting the SWRC functions to the observed data-points in order to optimize their parameters. However, the variance of SWRC data varies in different water contents; therefore, unlike the wet-end of the SWRC, the ULS method may not be sufficiently effective in estimating its dry-end. This study examined the differences between parameter approximations achieved by the ULS and the weighted least-squares (WLS) in the SWRC. Then, an analysis of both approaches in the simulation of water redistribution and the related soil physical quality indicators (SPQIs) was done. Accordingly