Find research datasets worth reusing

The impact of mistranslation on phenotypic variability and fitness

Phenotypic variation is widespread in natural populations, and can significantly alter their ecology and evolution. Phenotypic variation often reflects underlying genetic variation, but also manifests via non-heritable mechanisms. For instance, translation errors result in about 10% of cellular proteins carrying altered sequences. Thus, proteome diversification arising from translation errors can potentially generate phenotypic variability, in turn increasing variability in the fate of cells or of populations. However, the link between proteome diversity and phenotypic variability remains unverified. We manipulated mistranslation levels in Escherichia coli, and measured phenotypic variability between single cells (individual level variation), as well as replicate populations (population level variation). Monitoring growth and survival, we find that mistranslation indeed increases variation across E. coli cells, but does not consistently increase variability in growth parameters across replicate populations. Interestingly, although any deviation from the wild type (WT) level of mistranslation reduces fitness in an optimal environment, the increased variation is associated with a survival benefit under stress. Hence, we suggest that mistranslation-induced phenotypic variation can impact growth and survival and has the potential to alter evolutionary trajectories.

Data for: Pendulum-based measurements reveal impact dynamics at the scale of a trap-jaw ant

Small organisms can produce powerful, sub-millisecond impacts by moving tiny structures at high accelerations. We developed and validated a pendulum device to measure the impact energetics of microgram-sized trap-jaw ant mandibles accelerated against targets at 105 m s-2. Trap-jaw ants (Odontomachus brunneus; 19 individuals; 212 strikes) were suspended on one pendulum and struck swappable targets that were either attached to an opposing pendulum or fixed in place. Mean post-impact kinetic energy (energy from strike converted to pendulum motion) was higher with a stiff target (21.0-21.5 µJ) than a compliant target (6.4-6.5 µJ). Target mobility had relatively little influence. Mean contact duration of strikes against stiff targets was shorter (3.9-4.5 ms) than against compliant targets (6.2-7.9 ms). Shorter contact duration was correlated with higher post-impact kinetic energy. These findings contextualize and provide an energetic explanation for the diverse, natural uses of trap-jaw ant strikes such as impaling prey, launching away threats, and performing mandible-powered jumps. The strong effect of target material on energetic exchange suggests material interactions as an avenue for tuning performance of small, high acceleration impacts. Our device offers a foundation for novel research into the ecomechanics and evolution of tiny biological impacts and their application in synthetic systems.

Measurement Report: Strong Impacts of Biomass Burning, Nitrogen Fertilization, and Fine Particles on Gas-phase Hydrogen Peroxide (H2O2)

Measurement Report: Strong Impacts of Biomass Burning, Nitrogen Fertilization, and Fine Particles on Gas-phase Hydrogen Peroxide (H2O2)

Assessing the impact of static and fluctuating ocean acidification on the behavior of Amphiprion percula

Attached is the complete raw data from Vaughan and Dixson 2021 ‘Assessing the impact of static and fluctuating ocean acidification on the behavior of Amphiprion percula’.  Data collected from the behavioral lateralization trials has been inputted into the file ‘Vaughan_2020_Lateralization_Raw’. Column A indicate the CO2 treatment group, where “SPD” = Static Present Day, “SFD” = Static Future Day, “FPD” = Fluctuating Present Day, and “FFD” = Fluctuating Future Day. Each individual fish used from each treatment group (n=30) is displayed in Column B. Column C shows the binary results, in order, of each fish’s turns in the T-maze, and was scored as 0 (right turn) or 1 (left turn) for a total of 10 turns. The total number of turns to the right and left are provided in Column D-E. The relative lateralization (LR) of each fish was calculated {LR = [(Turn to the right – Turn to the left)/(Turn to the right + Turn to the left)] &lowast; 100} in Column F. Absolute lateralization (LA) is provided in Column G. Chemosensory response data has been inputted into the file ‘Vaughan_2020_Chemosensory_Raw’. Column A and B display treatment group and fish ID (n=20) as outlined above. The cue used in trial of either Tang (nonpredator) or Cod (predator) is provided in Column C, and the control in Column D. Numbers in these are used solely for the purpose of data analysis. The side of the cue in the flume is provided in Column E, and corresponds with the cue labelled in Column C. Buckets containing either the cue or control were placed above the flume and color coded as “BS” (blue side) and “RS” (red side), as the person scoring the trials was blinded. This also helped account for the switch (from one side of the flume to the other) that occurs halfway through each trial. Columns F-G represent results from the first 2min recording period, and Columns H-I represent results from the second 2min recording period. The total tallies from each fish are provided in Column J; the totals from each side are calculated in Columns K-L, and then sorted by either cue or control in Columns M-N. Proportions and percentages in cue and control are calculated and provided in Columns O-P and Q-R, respectively.  Carbonate chemistry data is compiled and provided in the ‘Vaughan_2020_Carbonate_Chemistry’. Measurements were taken each week (Column A) of each treatment group (as stated above, Column B). Column C reflects the time recordings were taken in the fluctuating treatments to hit the high, mid and low CO2 points at “6:30”, “12:30” and “18:30”. Measurements of static treatment groups were taken at randomly selected times to get the reflection of the carbonate chemistry of these treatments, but for the purpose of clarity in this document they are listed as “Static”. Measurements were taken from a subset of tanks each that rotated each week (Column D). Our target pHNBS values (i.e. what was programmed into the APEX System) are listed in Column E. Columns F-H displayed pHNBS (taken with APEX probes), temperature °C (taken with a portable Mettler Toledo probe) and salinity (taken with a refractometer). Water samples were analyzed spectrophotometrically to provide pHT and dissolved inorganic carbon, with values provided in Columns I-J. Using the program CO2SYS, total alkalinity and pCO2 were calculated, with values provided in Columns K-L.

Philornis parasitism: impact on nestlings and risk factors involved

Parasitic botfly larvae (Philornis ssp., Diptera: Muscidae) are found in nests of several bird taxa, although prevalence and nestling tolerance vary considerably among species. Here we describe patterns of botfly infestation in blue-black grassquit (Volatinia jacarina) nestlings. We identified the most typically affected nestling body parts and assessed parasite prevalence, impact on nestling survival, changes in nestling body shape and mass index. Additionally, we tested whether climatic conditions, nest morphology and habitat characteristics are associated with larvae abundance. Blue-black grassquits had low breeding success (15%), but most failures resulted from predation by vertebrate predators. We estimated that only 1% of nestlings died due to botfly infestation, and the number of larvae in nestling body did not affect nest success. Infected chicks exhibited a higher body mass to tarsus length ratio, and higher tarsus asymmetry. Previous studies indicate that adult grassquits with a higher body mass index have lower dominance status and mating success. Thus, we argue that although botflies had a small impact on offspring survival, they may reduce fitness in adulthood. There was no evidence that environmental conditions and nest morphology are linked to the number of larvae on nestlings. Territories with higher food supply had lower infestation rates. Possibly, food-rich habitats allow parents to invest more time in offspring care (brooding nestlings), thus protecting them from fly attacks. The present study brings to light new perspectives concerning bird-botfly interaction

The Early Childhood Education and Care COVID-19 Impact Study

This survey was designed to address the gap in knowledge around the impact that the COVID-19 global pandemic has had on Early Childhood Education and Care (ECEC) policy, practice and provision across the UK.  The survey explores the extent to which changes have been made in early years education and care settings and the perceptions of these changes among practitioners. The survey asked for perceptions about the impact of COVID-19 on staff, the children in their care (aged 0-8) and on their setting as a whole.

Data from: What factors increase the vulnerability of native birds to the impacts of alien birds?

This dataset accompanies a published paper (Evans et al. 2021) which aims to identify the factors that influence the vulnerability of native bird species to the impacts of alien bird species. In this paper we used mixed-effects models to test 14 variables that we hypothesised to influence vulnerability: this is a dataset of the 14 varaibles. We carried out our analyses using ten sets of these 14 variables: we provide all ten sets of these variables here. Please refer to Evans at al. (2021) for details on the methods used. An abstract to the published paper follows. Biodiversity impacts caused by alien species can be severe, including those caused by alien birds. In order to protect native birds, we aimed to identify factors that influence their vulnerability to the impacts of alien birds. We first reviewed the literature to identify native bird species sustaining such impacts. We then assigned impact severity scores to each native bird species, depending on the severity of the impacts sustained, and performed two types of analyses. First, we used contingency table tests to examine the distribution of impacts across their severity, type and location, and across native bird orders. Second, we used mixed-effects models to test factors hypothesised to influence the vulnerability of native birds to the impacts of alien birds. Ground-nesting shorebirds and seabirds were more prone to impacts through predation, while cavity-nesting woodpeckers and parrots were more prone to impacts through competition. Native bird species were more vulnerable when they occupied islands, warm regions, regions with climatic conditions similar to those in the native range of the invading alien species, and when they were physically smaller than the invading alien species. To a lesser extent, they were also vulnerable when they shared habitat preferences with the invading alien species. By considering the number and type of native bird species affected by alien birds, we demonstrate predation impacts to be more widespread than previously indicated, but also that damaging predation impacts may be underreported. We identify vulnerable orders of native birds, which may require conservation interventions; characteristics of native birds that increase their vulnerability, which may be used to inform risk assessments; and regions where native birds are most vulnerable, which may direct management interventions. The impacts sustained by native birds may be going unnoticed in many regions of the world: there is a clear need to identify and manage them.

opencc-byJan 2021View details →

Fault interaction and its impact on crustal extrusion in southeastern Tibetan Plateau: insights from geodynamical numerical modeling

Files include the data of the numerical model and model results of all cases in the study.

Hugoniot and released state of calcite above 200 GPa at planetary impact condition

Data include equation of state and adiabatic release state of shocked calcite. All data are gathered in a single Excel spreadsheet with multiple tabs.

Cumulative impacts of land cover change and dams on the land-water interface of the Tocantins River

This dataset accompanies the manuscript entitled "Cumulative impacts of land cover change and dams on the land-water interface of the Tocantins River". It contains shapefiles and geoTIFF files.

Impacts of ambient temperature and clutch size on incubation behaviour onset in a female-only incubator songbird

Ambient temperature is assumed to be the major cue used by passerines to synchronize their laying and hatching dates to the expected peak of prey availability. While laying eggs, females are still able to fine-tune their hatching date following increasing or decreasing patterns of ambient temperature, mostly via changes in incubation onset. The onset of incubation behaviour in relation to the laying sequence could have later consequences for the duration of the incubation period and the extent of hatching asynchrony. Clutch size is also known to affect incubation patterns and might therefore condition potential responses to changing temperatures. In this study we assessed the effect of ambient temperature and clutch size on the onset of four different incubation behaviours: partial and full nocturnal incubation, and partial and full diurnal incubation. We also evaluated the effect of the onset and duration of each incubation behaviour on the total duration of diurnal full incubation and the extent of hatching asynchrony. To achieve our aims, we monitored incubation behaviour using temperature data loggers during the egg laying period in three Mediterranean Great Tit Parus major populations in three consecutive years. Our results showed that increasing temperatures were related to an advance of diurnal partial incubation, but not to its duration, nor to the onset of full incubation behaviour. We did not find any effect of ambient temperatures on nocturnal incubation. However, females lengthened nocturnal partial incubation and delayed the onset of nocturnal full and diurnal partial incubation, when laying larger clutches. Longer diurnal incubation before clutch completion was associated with greater hatching asynchrony. Moreover, longer diurnal partial incubation shortened the duration of the full incubation period. In conclusion, increasing ambient temperatures during the egg-laying period advanced diurnal partial incubation, indirectly shortening the full incubation period and increasing hatching asynchrony.

opencc-zeroFeb 2021View details →

Impact of Pleistocene eustatic fluctuations on evolutionary dynamics in Southeast Asian biodiversity hotspots

Pleistocene Climatic Fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. While there is ample evidence of the impact of PCF on biodiversity for continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species diversity and endemism. Emergent land in Southeast Asia varied drastically with sea level fluctuations during the Pleistocene. Climate-induced fluctuations in sea level caused temporary connections between insular and continental biodiversity hotspots in Southeast Asia. These exposed lands likely had freshwater drainage systems that extended between modern islands: the Paleoriver Hypothesis. Built upon the assumption that aquatic organisms are among the most suitable models to trace ancient river boundaries and fluctuations of landmass coverage, the present study aims to examine the evolutionary consequences of PCF on the dispersal of freshwater biodiversity in Southeast Asia. Time-calibrated phylogenies of DNA-delimited species were inferred for six species-rich freshwater fish genera in Southeast Asia (Clarias, Channa, Glyptothorax, Hemirhamphodon, Dermogenys, Nomorhamphus). The results highlight rampant cryptic diversity and the temporal localization of most speciation events during the Pleistocene, with 88% of speciation events occurring during this period. Diversification analyses indicate that sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Ancestral area estimations point to Borneo as the most likely origin for most lineages, with two waves of dispersal to Sumatra and Java during the last 5 Myrs. Speciation events are more frequently associated with boundaries of the paleoriver watersheds, with 60%, than islands boundaries, with 40%. In total, one-third of speciation events are inferred to have occured within paleorivers on a single island, suggesting that habitat heterogeneity and factors other than allopatry between islands substantially affected diversification of Sundaland fishes. Our results suggest that species proliferation in Sundaland is not wholly reliant on Pleistocene sea-level fluctuations isolating populations on different islands.

opencc-by-4.0Feb 2021View details →

Is your OCR good enough? A comprehensive assessment of the impact of OCR quality on downstream tasks

Is an average OCR quality of 70% enough for my study? What OCR quality should we ask from external suppliers? Should we re-do the OCR of our collections to bring it from 80% to 85%? Libraries and researchers alike face the same dilemma in our times of textual abundance: when is OCR quality good enough? User access, scientific results and the investment of limited resources increasingly depend on answering this question. This project focuses on a comprehensive assessment of the impact of OCR quality in Dutch newspaper, journal and book collections, comparing it with published results for English and French. This is be done via extrinsic evaluation: assessing results from a set of representative downstream tasks, such as text classification or clustering. The ultimate goal of the project is to contribute guidelines detailing when OCR quality is to be considered good enough, in order to inform the development and use of textual collections. The datasets released here are described in <a href="https://github.com/Giovanni1085/KB_OCR_impact/wiki/Datasets">this Wiki page</a>. Please refer to the <a href="https://github.com/Giovanni1085/KB_OCR_impact">project's repository</a> for more information.

opencc-zeroDec 2012View details →

Data from: Night warming on hot days produces novel impacts on development, survival and reproduction in a small arthropod

1. An asymmetric increase of nighttime temperatures on hot days is one of the main features of global climate change. But the biological effects of an increased nighttime temperature combined with high daytime temperature are unclear. 2. We used six thermal regimens to simulate nighttime temperatures on hot days and investigated the effects of night warming on life history traits of the English grain aphid Sitobion avenae. Experimental temperatures fluctuated in continuous diurnal cycles, increasing from 27 °C to a maximum 35 °C and then declining to 27 °C gradually before further dropping to different minima (13, 16, 19, 21, 23 or 25 °C) representing nighttime temperatures. 3. When compared to expectations based on constant temperatures, night warming raised the optimum temperature for development by 3 °C, in contrast to results from experiments where temperature variability was altered symmetrically or in a parallel manner. Night warming also reduced aphid survival under heat from 75% to 37%, and depressed adult performance by up to 50%. Overall, night warming exacerbated the detrimental effects of hot days on the intrinsic rate of population increase, which was predicted to drop by 30% when nighttime minimum temperatures exceeded 20 °C. 4. Our novel findings on development challenge the 'Kaufmann effect', suggesting this is inapplicable to night warming likely to be encountered in nature. Although many average temperature models predict increasing pest outbreaks, our results suggest that outbreaks of some species might decrease due to the effects of night warming on population dynamics.

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 2015View details →

Data from: Forest degradation and invasive species synergistically impact Mimusops andongensis (Sapotaceae) in Lama Forest Reserve, Benin

Harvesting of Non-Timber Forest Products (NTFPs) can threaten target species, especially those with limited distribution and density. Exploited species also face threats from habitat fragmentation, fire, and invasive species. We assessed the impact of human disturbances and invasive species on the population of a key multipurpose NTFP species, Mimusops andongensis, in Lama Forest reserve (Benin). The densities of adult trees and regenerative stems decreased with increasing degradation. Mimusops andongensis contributed less to total tree density with increasing human disturbance. There were significantly fewer M. andongensis recruits with increasing cover of invasive Chromolaena odorata. Smaller diameter individuals predominated in non-degraded and moderately degraded sites while in degraded sites, the structure showed a negative exponential trend with the density of small diameter individuals being less than two trees/ha. Larger individuals were also rare in degraded sites. The low density of both mature trees and seedlings in degraded sites may undermine the long-term viability of M. andongensis, despite existing protection against NTFP harvesting and other anthropogenic pressures. Management should emphasize facilitating recruitment subsidies and limiting the presence of C. odorata.

opencc-zeroDec 2016View details →

Data from: Mauritius on fire: tracking historical human impacts on biodiversity loss

Fire was rare on Mauritius prior to human arrival (AD 1598); subsequently three phases of elevated fire activity occurred: c. 1630-1747, 1787-1833, and 1950-modern. Elevated fire frequency coincided with periods of high human impact evidenced from the historical record, and is linked to the extinction of island endemics.

opencc-zeroMay 2020View details →

Data from: Impact of brood parasitism and predation on nest survival of the fan-tailed gerygone in New Caledonia

Predation and brood parasitism are common reasons for nesting failure in passerine species and the additive impact by invasive species is a major conservation concern, particularly on tropical islands. Recognising the relative contribution of the different components of nesting failure rates is important to understand co-evolutionary interactions within brood parasite-host systems. In the remote archipelago of New Caledonia, the fan-tailed gerygone Gerygone flavolateralis is the exclusive host of the brood-parasitic shining bronze-cuckoo Chalcites lucidus. Additionally, invasive rodents also possibly have an impact on breeding success. To estimate the impact of potential nest predators, we 1) video monitored nests to identify predators, 2) estimated the probability of predation based on nest visibility and predator abundance and 3) tested the possibility that the location of experimental nests and lack of odour cues decrease the predation by rodents. In addition, we estimated nest survival rates using data collected in different habitats over the course of 8 breeding seasons. Nesting success of fan-tailed gerygone was relatively low and predation was the main cause of nesting failure. We recorded mainly predation by native birds, including the shining bronze-cuckoo, whereas predation by rats was rare. In open habitats predation by cuckoos was much lower than predation by other avian predators. Neither predator activity around nests nor nest visibility influenced the probability of predation. Experimental nests in more accessible locations and containing an odorous bait were more exposed to rodent predation. Apparently, the fan-tailed gerygone has either never been specifically vulnerable to predation by rats or has developed anti-predator adaptations.

opencc-zeroDec 2014View details →

Data from: Exploring the impact of habitat size on phylogeographic patterning in the Overberg velvet worm Peripatopsis overbergiensis (Onychophora: Peripatopsidae)

Evolutionary relationships in the velvet worm species, Peripatopsis overbergiensis, were examined in 3 forest areas in the Overberg region of South Africa to explore the impact of historical habitat fragmentation on the population genetic structure of the species. We collected 84 P. overbergiensis specimens from Grootvadersbosch, Koppie Alleen, and Marloth Nature Reserves and sequenced all these specimens for the cytochrome c oxidase subunit I (COI) locus, whereas a subset of 13 specimens were also sequenced for the 18S rRNA locus. Phylogenetic analyses of the 20 unique COI haplotypes revealed 4 genetically distinct clades, a result that is corroborated by the haplotype network. A hierarchical analysis of genetic variation was performed on the COI haplotype data within the 2 large forested areas, Grootvadersbosch and Marloth Nature Reserves, and across all 3 of the sample localities. These results revealed low haplotypic and nucleotide diversity within the largest Grootvadersbosch Nature Reserve forest and high haplotypic and nucleotide diversity within the fragmented Marloth Nature Reserve forest, whereas Koppie Alleen had the lowest haplotypic and nucleotide diversity. Across all 3 main localities statistically significant F ST values were found, together with the absence of shared haplotypes indicating the absence of maternal gene flow. Divergence time estimations based on the 20 COI haplotypes calculated in BEAST suggest a Pleistocene/Holocene divergence between the 4 clades as a result of habitat fragmentation and the aridification of the region. Our results indicate that conservation efforts should also prioritize linked, smaller fragmented habitats together with continuous habitats to maximize the genetic diversity of saproxylic fauna.