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Long-term adaptation of lymphoma cell lines to hypoxia is mediated by diverse molecular mechanisms that are targetable with specific inhibitors - Supplemental Data Tables
<p><strong>Supplemental Data Table - Metabolome.xlsx</strong> - a complete list of measured metabolites for Ramos and HBL2 cell lines. Peak area values for normoxic and hypoxia-adapted cells in triplicates. Mean log 2 fold change and adjusted P values are provided for all metabolites except those under the limits of detection.</p> <p><strong>Supplemental Data Table - Transcriptome Differential Expression.xlsx</strong> - the tables of all transcripts detected in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls. Fold change and log 2 fold change, log 2 CPM, F statistic, P value and False Discovery Rate (FDR) were calculated using EdgeR package. Last column shows if a transcript was significantly <em>up</em>- or <em>down</em>regulated or not (<em>ns</em>).</p> <p><strong>Supplemental Data Table - Transcriptome Gene Set Analysis.xlsx</strong> - the tables of the gene set enrichment analysis of Reactome pathways in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls.</p> <p><strong>Supplemental Data Table - Proteome Differential Expression.xlsx</strong> - the tables of proteins detected and differentially expressed in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls.</p> <p><strong>Supplemental Data Table - Cell lines SNV characterization.xlsx</strong> - the tables of mutations (single nucleotide variations and short indels) detected in four tested lymphpoma cell lines and corresponding primary tumor (PT) samples. AF_CTRL - allelic frequency (0..1) in healthy control DNA from the patient, AF_PT - allelic frequency in primary tumor, AF_PDCL - allelic frequency in patient-derived cell line. DP - total sequence depth, TLOD - Log odds that the variant is present in the tumor sample relative to the expected noise. Gencode and HGNC annotation columns are output of the Funcotator analysis. SNVs were detected using Mutect2 as a part of GATK 4.6.0.0 somatic variat calling pipeline.</p>
Supplements for Inferring Long-Term Tectonic Uplift Patterns from Bayesian Inversion of Fluvially-Incised Landscapes paper
<p><strong>Data and File Organization:</strong></p> <ol> <li><strong>Natural Landscapes (DEM):</strong> <ul> <li>Look for <code>.tif</code> files containing DEMs of natural landscapes. These files are in latitude-longitude coordinates; convert them to UTM if needed.</li> </ul> </li> <li><strong>Synthetic Landscapes (DEM):</strong> <ul> <li>DEM files for synthetic landscapes, ready for use in inversion schemes, are labeled with a <code>syn_</code> prefix.</li> </ul> </li> <li><strong>Climatic Data:</strong> <ul> <li>Climatic data for the Himalayas is available in <code>climate_data_him.zip</code>.</li> </ul> </li> </ol> <p><strong>Running the Code:</strong></p> <ol> <li> <p><strong>Loading DEMs:</strong></p> <ul> <li>Use the <code>loadDEM</code> package to load your DEM file.</li> <li>Specify <code>Z0</code> and <code>A0</code> values, then plot the landscape and <code>basinID</code> for reference.</li> </ul> </li> <li> <p><strong>Identifying Basins of Interest:</strong></p> <ul> <li>Determine which <code>basinID</code>s are of interest, then save them as forward objects. The functions for this process are available within the relevant packages.</li> </ul> </li> <li> <p><strong>Loading the Forward Model:</strong></p> <ul> <li>Load the forward model from the saved file using the appropriate function in the <code>frd</code> package.</li> <li>Choose the number of knots and specify if you prefer a 1D or 2D inversion.</li> </ul> </li> <li> <p><strong>Running and Plotting Inversion Results:</strong></p> <ul> <li>After running the inversion, view results in <code>inversion.step</code>.</li> <li>Plot these results using the plotting functions in the <code>frdplotting</code> package.</li> </ul> </li> </ol> <p> </p> <p> </p> <p><strong>Setup and Installation:</strong></p> <ul> <li>Install the package <code>scabbard</code> with: <div> <div> </div> <div><code>pip install pyscabbard </code></div> </div> </li> <li>All other Python dependencies are standard and can be installed via <code>pip</code> or <code>conda</code> as needed.</li> </ul>
Optimisation of RCA Content in Mortar Mixture Based on the Long-term Fracture and Fatigue Tests
<p>Data for the experimental study presented in: Optimisation of RCA Content in Mortar Mixture Based on the Long-term Fracture and Fatigue Tests</p>
Data for: Epigenetic Age and Long-Term Cancer Risk Following a Stroke
<p><strong>Data for Manuscript: "Epigenetic Age and Long-Term Cancer Risk Following a Stroke"</strong></p> <p>In this study, we investigated whether stroke patients who later developed cancer exhibited an accelerated epigenetic age compared to those who did not. A total of 648 stroke patients were followed for 15 years, during which 83 individuals were diagnosed with cancer. Biological age (B-age) was estimated from DNA methylation data derived from whole blood samples collected within 24 hours of stroke onset. These samples were analyzed using the 450K or EPIC Illumina Beadchip arrays. We employed several epigenetic clocks to calculate B-age, including the Hannum, Horvath, PhenoAge, ZhangBLUP, ZhangEN, and the mitotic epiTOC clocks.</p> <p>After adjusting for multiple testing, competing risks, and key confounders, we found that patients who developed cancer were biologically older, as measured by the Hannum clock.</p> <p>This repository provides the associated phenotypic data, estimated white cell counts and B-age estimations, including both raw data and age acceleration values.</p>
Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin
Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three years of common conditions, we find highly correlated expression patterns (Pearson's r = 0.992) among most genes. However, sixty-six genes were differentially expressed, including many ribosomal protein and biomineralization genes, all of which had higher expression in urchins originally from the southern population. Gene function analyses revealed slight but pervasive expression differences in genes related to ribosomal function, metabolism, transport, "bone" development, and response to stimuli. In accord with gene expression patterns, a post-hoc spine re-growth experiment revealed that urchins of southern origin re-grew spines at a faster rate than northern urchins. These results suggest that there may be genetically controlled, potentially adaptive differences in gene regulation across habitats and that gene expression differences may be under strong enough selection to overcome high dispersal-mediated gene flow in this marine species.
Data from: A phylogenetic and morphologic context for the radiation of an endemic fauna in a long-lived lake: Corbulidae (Bivalvia; Myoida) in the Miocene Pebas Formation of western Amazonia
The Corbulidae are one of a handful of a primarily marine bivalve clades that exhibit a remarkable radiation, marked by increased species richness and divergent morphologies, within a long-lived lake. For corbulids, this diversification occurred within the lower to middle Miocene Pebas Formation of western Amazonia. Only one taxon associated with this radiation (Anticorbula) remains extant. We conducted a series of phylogenetic analyses to characterize diversification of Corbulidae within the Pebas Formation and relate that diversification to geologically older freshwater corbulids from the Paleocene Fort Union Formation of the northern Great Plains (United States). We used these results, as well as a quantitative examination of morphospace occupation, to infer whether Pebasian corbulids represent a true species flock, and whether the lacustrine system represented by the Pebas Formation represents a cradle of, or reservoir for, freshwater corbulid diversity. We conducted two sets of phylogenetic analyses using shell morphology characters. A genus-level data set incorporated type species of freshwater corbulid genera, any Paleocene representatives of these genera, and selected brackish and marine corbulid genera. A species-level analysis added all described freshwater corbulid taxa to the genus-level matrix. Our results were highly resolved (few most-parsimonious trees), but not particularly robust (low branch support). For the genus-level matrix, we used a taxon jackknife procedure to explore the effects of taxon sampling on tree stability and topology. Jackknife results recover a subclade of freshwater taxa (including both Anticorbula and Pachydon species and the Paleocene Ostomya sp.) in 92.4% of trees, although placement of this subclade across the ingroup varies, as do the topologic positions of other freshwater species. Freshwater and marine corbulids also are morphologically distinct from each other, a factor that likely reduced the robustness of our phylogenetic results. By combining these results with paleoecologic, stratigraphic, and morphologic data, we infer that freshwater corbulids arose once within the family, prior to the Cenozoic, with three distinct freshwater lineages present at their first appearance in the late Paleocene of North America. Within the Miocene Pebas system of South America, we reconstruct supralimital morphologic evolution within three lineages as freshwater taxa became variously adapted to the fluid, dysoxic muds characterizing lake-bottom facies representative of the Pebas lacustrine system. In addition, corbulids apparently successfully coped with high predation pressures from co-occurring shellcrushing predators. Finally, we consider that freshwater Corbulidae were primarily fluvial taxa throughout their geologic history, with a relatively ephemeral radiation within the Pebasian lake system, thus making the Pebasian system a cradle of diversity for several corbulid lineages.
Data from: Bouldering: an alternative strategy to long-vertical climbing in root-climbing hortensias
In the Neotropics, the genus Hydrangea of the popular ornamental hortensia family is represented by climbing species that strongly cling to their support surface by means of adhesive roots closely positioned along specialized anchoring stems. These root-climbing hortensia species belong to the nearly exclusive American Hydrangea section Cornidia and generally are long lianescent climbers that mostly flower and fructify high in the host tree canopy. The Mexican species Hydrangea seemannii, however, encompasses not only long lianescent climbers of large vertical rock walls and coniferous trees, but also short 'shrub-like' climbers on small rounded boulders. To investigate growth form plasticity in root-climbing hortensia species, we tested the hypothesis that support variability (e.g. differences in size and shape) promotes plastic responses observable at the mechanical, structural and anatomical level. Stem bending properties, architectural axis categorization, tissue organization and wood density were compared between boulder and long-vertical tree-climbers of H. seemannii. For comparison, the mechanical patterns of a closely related, strictly long-vertical tree-climbing species were investigated. Hydrangea seemannii has fine-tuned morphological, mechanical and anatomical responses to support variability suggesting the presence of two alternative root-climbing strategies that are optimized for their particular environmental conditions. Our results suggest that variation of some stem anatomical traits provides a buffering effect that regulates the mechanical and hydraulic demands of two distinct plant architectures. The adaptive value of observed plastic responses and the importance of considering growth form plasticity in evolutionary and conservation studies are discussed.
Data from: Rock wrens preferentially use song types that improve long distance signal transmission during natural singing bouts
When animals are capable of producing variable signals they may preferentially use some signal types over others. Among songbirds, individuals are known to alter song type form and usage patterns in contest and mating situations, but studies have not examined how song choice improves signal efficacy during broadcast song. For this study we investigated rock wren Salpinctes obsoletus song type use rates during natural singing bouts. We tested three hypotheses for adaptive song use during broadcast song: 1) birds improve signal content by increasing the use of high quality songs, 2) birds optimize for signal propagation by preferentially using songs that transmit well, and 3) birds maintain energy by reducing the use of costly songs. The study included 19 058 songs sung by 12 individuals, each of which had a measured song repertoire of between 52 and 117 song types which were produced at highly variable rates. Results indicated that rock wrens did not preferentially sing song types with shorter durations or fewer frequency switches, as would be expected if they selected song types to minimize delivery costs. They also did not favor songs with more rapid trills or more frequency switches, as would be expected if they adjusted song use primarily to indicate quality. Focal birds did preferentially sing significantly longer songs with lower bandwidths, lower frequencies, and slower trill rates. Results suggest that natural broadcast singing patterns are shaped more by the benefits of long distance transmission than by the benefits of advertising performance ability or the costs of song production.
How long is 3 kilometres for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula
<p>1. Populations inhabiting Mediterranean islands often show contrasting genetic lineages, even on islands that were connected to the mainland during glacial maxima. This pattern is generated by forces acting in historical and contemporary times. Understanding these phenomena requires comparative studies relating genetic structure, functional traits and dispersal constraints.</p> <p>2. Using as a model the butterfly species living across the Messina strait separating Sicily from the Italian Peninsula (3 km wide), we aimed to unravel the mechanisms limiting the dispersal of matrilines across a narrow sea strait and producing genetic differentiation. </p> <p>3. We analysed the mitochondrial COI gene of 84 butterfly species out of 90 documented in Sicily and compared them with populations from the neighbouring southern Italian Peninsula (1398 sequences) and from the entire Palearctic region (8093 sequences). For each species, we regressed 13 functional traits and two ecological constraints to dispersal (winds experienced at the strait and climatic suitability) against genetic differentiation between Sicily and Italian Peninsula to understand the factors limiting dispersal.</p> <p>4. More than a third of the species showed different haplogroups across the strait and most of them also represented endemic haplogroups for this island. One fifth of Sicilian populations (and 32.3% of endemic lineages) had their closest relatives in distant areas, instead of the neighbouring Italian Peninsula, which suggests high relictuality. Haplotype diversity was significantly explained by length of the flight period, an intrinsic phenology trait, while genetic differentiation was explained by both intrinsic traits (wingspan and degree of generalism) and contemporary local constraints (winds experienced at the strait and climatic suitability).</p> <p>5. A relatively narrow sea strait can produce considerable differentiation among butterfly matrilines and this phenomenon showed a largely deterministic fingerprint. Because of unfavourable winds, populations of the less dispersive Sicilian butterflies tended to differentiate into endemic variants or to maintain relict populations. Understanding these phenomena required the integration of DNA sequences, species traits and physical constraints for a large taxon at continental scale. Future studies may reveal if the patterns here shown for mitochondrial DNA are also reflected in the nuclear genome or, alternatively, are the product of limited female dispersal.</p>
Data from: Population signatures of large-scale, long-term disjunction and small-scale, short-term habitat fragmentation in an Afromontane forest bird
The Eastern Afromontane cloud forests occur as geographically distinct mountain exclaves. The conditions of these forests range from large to small and from fairly intact to strongly degraded. For this study, we sampled individuals of the forest bird species, the Montane White-eye Zosterops poliogaster from 16 sites and four mountain archipelagos. We analysed 12 polymorphic microsatellites and three phenotypic traits, and calculated Species Distribution Models (SDMs) to project past distributions and predict potential future range shifts under a scenario of climate warming. We found well-supported genetic and morphologic clusters corresponding to the mountain ranges where populations were sampled, with 43% of all alleles being restricted to single mountains. Our data suggest that large-scale and long-term geographic isolation on mountain islands caused genetically and morphologically distinct population clusters in Z. poliogaster. However, major genetic and biometric splits were not correlated to the geographic distances among populations. This heterogeneous pattern can be explained by past climatic shifts, as highlighted by our SDM projections. Anthropogenically fragmented populations showed lower genetic diversity and a lower mean body mass, possibly in response to suboptimal habitat conditions. On the basis of these findings and the results from our SDM analysis we predict further loss of genotypic and phenotypic uniqueness in the wake of climate change, due to the contraction of the species' climatic niche and subsequent decline in population size.
Data from: A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction
Size is among the most important traits of any organism, yet the factors that control its evolution remain poorly understood. In this study, we investigate controls on the evolution of organismal size using a newly compiled database of nearly 25,000 foraminiferan species and subspecies spanning the past 400 million years. We find a transition in the pattern of foraminiferan size evolution from correlation with atmospheric pO2 during the Paleozoic (400-250 Mya) to long-term stasis during the post-Paleozoic (250 Mya to present). Thus, a dramatic shift in the evolutionary mode coincides with the most severe biotic catastrophe of the Phanerozoic (543 Mya to present). Paleozoic tracking of pO2 was confined to Order Fusulinida, whereas Paleozoic lagenides, miliolids, and textulariids were best described by the stasis model. Stasis continued to best describe miliolids and textulariids during post-Paleozoic time, while random walk was the best supported mode for the other diverse orders. The shift in evolutionary dynamics thus appears to have resulted primarily from the selective elimination of fusulinids at the end of the Permian Period. These findings illustrate the potential for mass extinction to alter macroevolutionary dynamics for hundreds of millions of years.
Data from: Pattern of polyphenol intake and the long-term risk of dementia in older persons
Objective: To investigate the optimal combination of dietary polyphenols associated with the long-term risk of dementia in a large prospective French cohort of older persons, the Three-City (3C) Study. Methods: We included 1,329 non-demented older adults from the 3C Study with assessment of intake of 26 polyphenol subclasses and followed for 12 years for dementia. Using Partial Least Square for Cox models, we identified a pattern of polyphenol intake associated with dementia risk. Results: The pattern combined several flavonoids (dihydroflavonols, anthocyanins, isoflavonoids, flavanones), stilbenes (including resveratrol), lignans and other subclasses (hydroxybenzaldehydes, naphtoquinones, furanocoumarins). Compared with participants in the lower quintile of pattern score, those in the higher quintile had a 50% lower risk of dementia (95% CI 20%; 68%, p-trend <0.01) in multivariate models. Conclusions: In this French cohort, a polyphenol pattern provided by a diet containing specific plant products (nuts, citrus, berries, leafy vegetables, soy, cereals, olive oil) accompanied with red wine and tea was associated with lower dementia risk.
Data from: A mimicked bacterial infection prolongs stopover duration in songbirds – but more pronounced in short- than long-distance migrants
1) Migration usually consists of intermittent travel and stopovers, the latter being crucially important for individuals to recover and refuel to successfully complete migration. Quantifying how sickness behaviours influence stopovers is crucial for our understanding of migration ecology and how diseases spread. However, little is known about infections in songbirds, which constitute the majority of avian migrants. 2) We experimentally immune-challenged autumn migrating passerines (both short- and long-distance migrating species) with a simulated bacterial infection. Using an automated radio-telemetry system in the stopover area, we subsequently quantified stopover duration, 'bush-level' activity patterns (0.1-30m) and landscape movements (30-6000m). 3) We show that compared to controls, immune-challenged birds prolonged their stopover duration by on average 1.2 days in long-distance and 2.9 days in short-distance migrants, respectively (100 – 126 % longer than controls, respectively). During the prolonged stopover, the immune-challenged birds kept a high 'bush-level' activity (which was unexpected) but reduced their local movements, independent of migration strategy. Baseline immune function, but not blood parasite infections prior to the immune challenge, had a prolonging effect on stopover duration, particularly in long-distance migrants. 4) We conclude that a mimicked bacterial infection does not cause lethargy, per se, but restricts landscape movements and prolongs stopover duration, and that this behavioural response also depends on the status of baseline immunity and migration strategy. This adds a new level to the understanding of how acute inflammation affect migration behaviour and hence the ecology and evolution of migration. Accounting for these effects of bacterial infections will also enable us to fine-tune and apply optimal migration theory. Finally it will help us predicting how migrating animals may respond to increased pathogen pressure by global change.
Data from: Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea
Plant–soil interactions are increasingly recognized to play a major role in terrestrial ecosystems functioning. However, few studies to date have focused on slow dynamic ecosystems such as forests. As they are vertically stratified by multiple vegetation strata, canopy tree removal by thinning operations could alter forest plant community through tree canopy opening. Very little is known about cascading effects on soil biodiversity. We conducted a large-scale, multi-site assessment of collembolan assemblage response to long-term canopy tree removal in sessile oak Quercus petraea temperate forests. A total of 33 experimental plots were studied covering a large gradient of canopy tree basal area, stand age and local abiotic contexts. Collembolan abundance strongly declined with canopy tree removal in early forest successional stage and this was mediated by negative effect of understory plant community composition changes, i.e. shift from moss and forb to tree seedling, fern, shrub and grass species. Negative effect of this composition shift on collembolan species richness was largely offset by positive effect of the increase in understory plant species richness. This gives support to both the plant mass-ratio and functional diversity hypotheses. Collembolan functional groups had contrasting response patterns, which were mediated by different ecological factors. Epedaphic (r-strategist) abundance and species richness increased with canopy tree removal in relation with the increase in understory plant species richness. In contrast, euedaphic (K-strategist) abundance and species richness declined with canopy tree removal in early forest successional stage in relation with changes in understory plant community composition and species richness, as well as microclimatic conditions. Overall, our study provides experimental evidence that forest plant community can be a strong driver of collembolan assemblages. It also emphasizes the role of trees as foundation species of forest ecosystems that can shape soil biodiversity through their regulation of understory plant community and ecosystem abiotic conditions.
Data from: A framework for the identification of long-term social avoidance in longitudinal datasets
Animal sociality is of significant interest to evolutionary and behavioural ecologists, with efforts focused on the patterns, causes and fitness outcomes of social preference. However, individual social patterns are the consequence of both attraction to (preference for) and avoidance of conspecifics. Despite this, social avoidance has received far less attention than social preference. Here, we detail the necessary steps to generate a spatially explicit, iterative null model which can be used to identify non-random social avoidance in longitudinal studies of social animals. We specifically identify and detail parameters which will influence the validity of the model. To test the usability of this model, we applied it to two longitudinal studies of social animals (Eastern water dragons (Intellegama leseurii) and bottlenose dolphins (Tursiops aduncus) to identify the presence of social avoidances. Using this model allowed us to identify the presence of social avoidances in both species. We hope that the framework presented here inspires interest in addressing this critical gap in our understanding of animal sociality, in turn allowing for a more holistic understanding of social interactions, relationships and structure.
Data from: Phylogeography of Bornean land snails suggests long-distance dispersal as a cause of endemism
Aim: Islands are often hotspots of endemism due to their isolation, making colonization a rare event, and hence facilitating allopatric speciation. Dispersal usually occurs between nearby locations according to a stepping-stone model. We aimed to reconstruct colonization and speciation processes in an endemic-rich system of land-based islands that does not seem to follow the obvious stepping-stone model of dispersal. Location: Five land-based habitat archipelagos of limestone outcrops in the floodplain of the Kinabatangan River in Sabah, Malaysian Borneo. Methods: We studied the phylogeography of three species complexes of endemic land snails, using multiple genetic markers. We calculated genetic distances between populations, applied BEAST2 to reconstruct phylogenies for each taxon, and subsequently reconstructed ancestral ranges using 'BIOGEOBEARS'. Results: We found spatial genetic structure among nearby locations to be highly pronounced for each taxon. Genetic correlation was present at small spatial scales only, and disappeared at distances of five kilometres and above. Most archipelagos have been colonized from within the region multiple times over the past three million years, in 78% of cases as a result of long-distance dispersal or dispersal from non-adjacent limestone outcrops. The flow of the main geographical feature within the region, the Kinabatangan River, did not play a role. Main conclusions: Phylogeographic structure in these Bornean land snails has only partly been determined by small-scale dispersal, where it leads to isolation-by-distance, but mostly by long-distance dispersal. Our results demonstrate that island endemic taxa only very locally follow a simple stepping-stone model, whilst dispersal to non-adjacent islands, and especially long-distance dispersal, is most important. This leads to the formation of highly localized, isolated "endemic populations" forming the onset of a complex radiation of endemic species.
Data from: Studying long-term, large-scale grassland restoration outcomes to improve seeding methods and reveal knowledge gaps
Studies are increasingly investigating effects of large-scale management activities on grassland restoration outcomes. These studies are providing useful comparisons among currently used management strategies, but not the novel strategies needed to rapidly improve restoration efforts. Here we illustrate how managing restoration projects adaptively can allow promising management innovations to be identified and tested. We studied 327 Great Plains fields seeded after coal mining. We modelled plant responses to management strategies to identify the most effective previously used strategies for constraining weeds and establishing desired plants. Then, we used the model to predict responses to new strategies our analysis identified as potentially more effective. Where established, the weed crested wheatgrass (Agropyron cristatum L.) increased through time, indicating a need to manage establishment of this grass. Seeding particular grasses reduced annual weed cover, and because these grasses appeared to become similarly abundant whether sown at low or high rates, low rates could likely be safely used to reduce seeding costs. More importantly, lower than average grass seed rates increased cover of shrubs, the plants most difficult to restore to many grassland ecosystems. After identifying grass seed rates as a driver, we formulated model predictions for rates below the range managers typically use. These predictions require testing but indicated atypically low grass seed rates would further increase shrubs without hindering long-term grass stand development. Synthesis and applications. Designing management around empirically based predictions is a logical next step towards improving ecological restoration efforts. Our predictions are that reducing grass seed rates to atypically low levels will boost shrubs without compromising grasses. Because these predictions derive from the fitted model, they represent quantitative hypotheses based on current understanding of the system. Generating data needed to test and update these hypotheses will require monitoring responses to shifts in management, specifically shifts to lower grass seed rates. A paucity of data for confronting hypotheses has been a major sticking point hindering adaptive management of most natural resources, but this need not be the case with degraded grasslands, because ongoing restoration efforts around the globe are providing continuous opportunities to monitor and manage processes regulating grassland restoration outcomes.
Data from: Context-dependent colonisation of terrestrial habitat 'islands' by a long-distance migrant bird
Landscape context can affect how individuals perceive patch quality during colonisation. However, although context-dependent colonisation has been observed in aquatic environments it has rarely been studied in terrestrial environments or at large spatial scales. Here, we assessed how landscape context influenced colonisation rates in a large-scale (c.7000 km2) terrestrial system where colonisers (Willow Warbler Phylloscopus trochilus) are capable of rapid, long-distance movements. Bioacoustic recorders were used to detect first song dates (an indicator of colonisation or re-colonisation) and settlement in 23 naturally replicated habitat patches. We compared support for three competing hypotheses describing colonisation patterns that depend on landscape context ('redirection', 'landscape-selection' and 'relative patch size') with two patch-level hypotheses (patch 'quality' and 'heterospecific attraction'). First song was earlier when habitat availability in the landscape was low, supporting the 'redirection' hypothesis. Settlement probability was best predicted by patch 'quality' and was lower in woodlands with a dense understorey. Results suggest that colonisation of habitat patches by male P. trochilus after spring migration is spatially hierarchical. First, initial colonisation depends on landscape context, and settlement is then determined by fine-scale vegetation characteristics. More broadly, we suggest that patterns observed in fragmented aquatic environments (e.g. 'redirection') can, in some circumstances, be extended to large-scale terrestrial environments.
Data from: Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?
Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.
Data from: AviaNZ: a future-proofed program for annotation and recognition of animal sounds in long-time field recordings
The routine collection of long‐time acoustic recordings of animals in the field presents new challenges in data analysis. While many terabytes of data are collected annually, effective use of this noisy, highly variable data require skilled humans to manually identify calls. While computer programs to automatically analyse these recordings are becoming available, it is important that they are user‐friendly and easy‐to‐use, so that everybody – citizen scientists, wildlife managers, researchers – can take advantage of them, and that they keep the human in the loop so analyses carried out this year are comparable both to manual call counts from the past, and more accurate automated analyses performed in the future. We present the AviaNZ program, which is designed to achieve these goals: the software includes methods for simple, rapid manual annotation of recordings, denoising and segmentation methods, and a training procedure by which the user can prepare their own filters to automatically recognize individual species. The software can run in batch mode, automatically processing folders of field recordings, and then present the outputs to enable the quick and easy review of the results. Finally, the outputs are presented in a variety of spreadsheets to enable different statistical analyses to be performed. We describe the various workflows of manually and semi‐automatically processing sound files, annotating them to train automatic filters, using those filters in batch mode, and how the software facilitates rapid evaluation of the automated analysis. A demonstration of the software, comparing manual and automatic detection of calls of the little spotted kiwi Apteryx owenii is given. It shows that while the automatic detection does produce false positives, human correction of these is far faster than manual review of the whole sound file. AviaNZ is a freely available open‐source standalone program. Our experience shows that it can be used by anybody quickly and easily. However, for experienced users it is easily customizable and extendable. By enabling everybody involved with acoustic bird recording to quickly and easily analyse their own data, while future‐proofing it by keeping the human in the loop, we are enabling acoustic field recordings to meet their potential.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.