cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12625940
title: Schmoll Proc B ESM R Code.txt from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: In species with internal fertilization, the female genital tract appears challenging to sperm, possibly resulting from selection on for example ovarian fluid to control sperm behaviour and, ultimately, fertilization. Few studies, however, have examined the effects of swimming media viscosities on sperm performance. We quantified effects of media viscosities on sperm velocity in promiscuous willow warblers <i>Phylloscopus trochilus</i>. We used both a reaction norm and a character-state approach to model phenotypic plasticity of sperm behaviour across three experimental media of different viscosities. Compared to a standard medium (Dulbecco's Modified Eagle Medium, DMEM), media enriched with 1% or 2% w/v methyl cellulose decreased sperm velocity by up to about 50%. Spermatozoa from experimental ejaculates of different males responded similarly to different viscosities, and a lack of covariance between elevations and slopes of individual velocity-by-viscosity reaction norms indicated that spermatozoa from high- and low-velocity ejaculates were slowed down by a similar degree when confronted with high-viscosity environments. Positive cross-environment (1% versus 2% cellulose) covariances of sperm velocity under the character-state approach suggested that sperm performance represents a transitive trait, with rank order of individual ejaculates maintained when expressed against different environmental backgrounds. Importantly, however, a lack of significant covariances in sperm velocity involving a cellulose concentration of 0% indicated that pure DMEM represented a qualitatively different environment, questioning the validity of this widely used standard medium for assaying sperm performance. Enriching sperm environments along ecologically relevant gradients prior to assessing sperm performance will strengthen explanatory power of <i>in vitro</i> studies of sperm behaviour.
DOI: 10.6084/m9.figshare.12626024
title: Raw data from Evolution of drug-resistant and virulent small colonies in phenotypically diverse populations of the human fungal pathogen <i>Candida glabrata</i>

description: Antimicrobial resistance frequently carries a fitness cost to a pathogen, measured as a reduction in growth rate compared to the sensitive wild-type, in the absence of antibiotics. Existing empirical evidence points to the following relationship between cost of resistance and virulence. If a resistant pathogen suffers a fitness cost in terms of reduced growth rate it commonly has lower virulence compared to the sensitive wild-type. If this cost is absent so is the reduction in virulence. Here we show, using experimental evolution of drug resistance in the fungal human pathogen <i>Candida glabrata,</i> that reduced growth rate of resistant strains need not result in reduced virulence. Phenotypically heterogeneous populations were evolved in parallel containing highly resistant sub-population small colony variants (SCVs) alongside sensitive sub-populations. Despite their low growth rate in the absence of an antifungal drug, the SCVs did not suffer a marked alteration in virulence compared with the wild-type ancestral strain, or their co-isolated sensitive strains. This contrasts with classical theory that assumes growth rate to positively correlate with virulence. Our work thus highlights the complexity of the relationship between resistance, basic life-history traits and virulence.
DOI: 10.6084/m9.figshare.12627140.v2
title: MODFLOW-OWHM_v2_Across_the_US

description: Modeling the Surface Water and Groundwater Budgets of the US using MODFLOW-OWHM
DOI: 10.6084/m9.figshare.12625940.v1
title: Schmoll Proc B ESM R Code.txt from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: In species with internal fertilization, the female genital tract appears challenging to sperm, possibly resulting from selection on for example ovarian fluid to control sperm behaviour and, ultimately, fertilization. Few studies, however, have examined the effects of swimming media viscosities on sperm performance. We quantified effects of media viscosities on sperm velocity in promiscuous willow warblers <i>Phylloscopus trochilus</i>. We used both a reaction norm and a character-state approach to model phenotypic plasticity of sperm behaviour across three experimental media of different viscosities. Compared to a standard medium (Dulbecco's Modified Eagle Medium, DMEM), media enriched with 1% or 2% w/v methyl cellulose decreased sperm velocity by up to about 50%. Spermatozoa from experimental ejaculates of different males responded similarly to different viscosities, and a lack of covariance between elevations and slopes of individual velocity-by-viscosity reaction norms indicated that spermatozoa from high- and low-velocity ejaculates were slowed down by a similar degree when confronted with high-viscosity environments. Positive cross-environment (1% versus 2% cellulose) covariances of sperm velocity under the character-state approach suggested that sperm performance represents a transitive trait, with rank order of individual ejaculates maintained when expressed against different environmental backgrounds. Importantly, however, a lack of significant covariances in sperm velocity involving a cellulose concentration of 0% indicated that pure DMEM represented a qualitatively different environment, questioning the validity of this widely used standard medium for assaying sperm performance. Enriching sperm environments along ecologically relevant gradients prior to assessing sperm performance will strengthen explanatory power of <i>in vitro</i> studies of sperm behaviour.
DOI: 10.6084/m9.figshare.12626024.v1
title: Raw data from Evolution of drug-resistant and virulent small colonies in phenotypically diverse populations of the human fungal pathogen <i>Candida glabrata</i>

description: Antimicrobial resistance frequently carries a fitness cost to a pathogen, measured as a reduction in growth rate compared to the sensitive wild-type, in the absence of antibiotics. Existing empirical evidence points to the following relationship between cost of resistance and virulence. If a resistant pathogen suffers a fitness cost in terms of reduced growth rate it commonly has lower virulence compared to the sensitive wild-type. If this cost is absent so is the reduction in virulence. Here we show, using experimental evolution of drug resistance in the fungal human pathogen <i>Candida glabrata,</i> that reduced growth rate of resistant strains need not result in reduced virulence. Phenotypically heterogeneous populations were evolved in parallel containing highly resistant sub-population small colony variants (SCVs) alongside sensitive sub-populations. Despite their low growth rate in the absence of an antifungal drug, the SCVs did not suffer a marked alteration in virulence compared with the wild-type ancestral strain, or their co-isolated sensitive strains. This contrasts with classical theory that assumes growth rate to positively correlate with virulence. Our work thus highlights the complexity of the relationship between resistance, basic life-history traits and virulence.
DOI: 10.6084/m9.figshare.12626025.v1
title: Genome wide association analyses for <i>Jenynsia lineata</i> (a) and <i>Anableps dowei</i> (b,c,d,e). from The direction of genital asymmetry is expressed stochastically in internally fertilizing anablepid fishes

description: These tables contain the results of the association mapping conducted using PLINK for <i>Jenynsia lineata</i> (a), all specimens of <i>Anableps dowei</i> combining compatible breeding morphs for males and females (b), all specimens of <i>A. dowei</i> combining incompatible breeding morphs for males and females (c), only males of <i>A. dowei</i> (d), and only females of <i>A. dowei</i> (e).
DOI: 10.6084/m9.figshare.12625931
title: Data File from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12625934
title: Schmoll Proc B ESM ASReml Code_pin.txt from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Electronic supplementary Tables and Figures;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 0% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 1% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 2% cellulose;Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12625931.v1
title: Data File from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12625922
title: Schmoll Proc B ESM ASReml Code_as.txt from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Electronic supplementary Tables and Figures;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 0% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 1% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 2% cellulose;Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12625934.v1
title: Schmoll Proc B ESM ASReml Code_pin.txt from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Electronic supplementary Tables and Figures;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 0% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 1% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 2% cellulose;Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12625922.v1
title: Schmoll Proc B ESM ASReml Code_as.txt from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Electronic supplementary Tables and Figures;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 0% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 1% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 2% cellulose;Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12625914
title: Study Data from Explicit characterization of human population connectivity reveals long run persistence of interregional dengue shocks

description: Dengue is hyper-endemic in Singapore and Malaysia, and daily movement rates between the two countries are consistently high, allowing inference on the role of local transmission and imported dengue cases. This paper describes a custom built sparse space—time autoregressive (SSTAR) model to infer and forecast contemporaneous and future dengue transmission patterns in Singapore and 16 administrative regions within Malaysia, taking into account connectivity and geographical adjacency between regions as well as climatic factors. A modification to forecast impulse responses is developed for the case of the SSTAR and is used to simulate changes in dengue transmission in neighbouring regions following a disturbance. The results indicate that there are long-term responses of the neighbouring regions to shocks in a region. By computation of variable inclusion probabilities, we found that each region’s own past counts were important to describe contemporaneous case counts. In 15 out of 16 regions, other regions case counts were important to describe contemporaneous case counts even after controlling for past local dengue transmissions and exogenous factors. Leave-one-region out analysis using SSTAR showed that dengue transmission counts could be reconstructed for 13 of 16 regions counts using external dengue transmissions compared to a climate only approach. Lastly, one to four week ahead forecasts from the SSTAR were more accurate than baseline univariate autoregressions.
DOI: 10.6084/m9.figshare.12625914.v1
title: Study Data from Explicit characterization of human population connectivity reveals long run persistence of interregional dengue shocks

description: Dengue is hyper-endemic in Singapore and Malaysia, and daily movement rates between the two countries are consistently high, allowing inference on the role of local transmission and imported dengue cases. This paper describes a custom built sparse space—time autoregressive (SSTAR) model to infer and forecast contemporaneous and future dengue transmission patterns in Singapore and 16 administrative regions within Malaysia, taking into account connectivity and geographical adjacency between regions as well as climatic factors. A modification to forecast impulse responses is developed for the case of the SSTAR and is used to simulate changes in dengue transmission in neighbouring regions following a disturbance. The results indicate that there are long-term responses of the neighbouring regions to shocks in a region. By computation of variable inclusion probabilities, we found that each region’s own past counts were important to describe contemporaneous case counts. In 15 out of 16 regions, other regions case counts were important to describe contemporaneous case counts even after controlling for past local dengue transmissions and exogenous factors. Leave-one-region out analysis using SSTAR showed that dengue transmission counts could be reconstructed for 13 of 16 regions counts using external dengue transmissions compared to a climate only approach. Lastly, one to four week ahead forecasts from the SSTAR were more accurate than baseline univariate autoregressions.
DOI: 10.6084/m9.figshare.12625907
title: Supplementary Figure S2 from Bioinformatical dissection of fission yeast DNA replication origins

description: Supplementary Figure S2, related to Figure 6
DOI: 10.6084/m9.figshare.12625907.v1
title: Supplementary Figure S2 from Bioinformatical dissection of fission yeast DNA replication origins

description: Supplementary Figure S2, related to Figure 6
DOI: 10.6084/m9.figshare.12625841
title: Supplementary material.zip from Speed oscillations in classical pilot-wave dynamics

description: We present the results of a theoretical investigation of a dynamical system consisting of a particle self-propelling through a resonant interaction with its own quasi-monochromatic pilot-wave field. We rationalize two distinct mechanisms, arising in different regions of parameter space, that may lead to a wavelike statistical signature with the pilot-wavelength. First, resonant speed oscillations with the wavelength of the guiding wave may arise when the particle is perturbed from its steady self-propelling state. Second, a random-walk-like motion may set in when the decay rate of the pilot-wave field is sufficiently small. The implications for the emergent statistics in classical pilot-wave systems are discussed.
DOI: 10.6084/m9.figshare.12625841.v2
title: Supplementary material.zip from Speed oscillations in classical pilot-wave dynamics

description: We present the results of a theoretical investigation of a dynamical system consisting of a particle self-propelling through a resonant interaction with its own quasi-monochromatic pilot-wave field. We rationalize two distinct mechanisms, arising in different regions of parameter space, that may lead to a wavelike statistical signature with the pilot-wavelength. First, resonant speed oscillations with the wavelength of the guiding wave may arise when the particle is perturbed from its steady self-propelling state. Second, a random-walk-like motion may set in when the decay rate of the pilot-wave field is sufficiently small. The implications for the emergent statistics in classical pilot-wave systems are discussed.
DOI: 10.6084/m9.figshare.12625841.v1
title: Supplementary material.zip from Speed oscillations in classical pilot-wave dynamics

description: We present the results of a theoretical investigation of a dynamical system consisting of a particle self-propelling through a resonant interaction with its own quasi-monochromatic pilot-wave field. We rationalize two distinct mechanisms, arising in different regions of parameter space, that may lead to a wavelike statistical signature with the pilot-wavelength. First, resonant speed oscillations with the wavelength of the guiding wave may arise when the particle is perturbed from its steady self-propelling state. Second, a random-walk-like motion may set in when the decay rate of the pilot-wave field is sufficiently small. The implications for the emergent statistics in classical pilot-wave systems are discussed.
DOI: 10.6084/m9.figshare.12625805
title: ESM S1 from How to escape from insect egg parasitoids: a review of potential factors explaining parasitoid absence across the Insecta

description: Location of host eggs by parasitoids and information on most important egg parasitoid genera, incl. figure S1
DOI: 10.6084/m9.figshare.12625808
title: ESM table S2 from How to escape from insect egg parasitoids: a review of potential factors explaining parasitoid absence across the Insecta

description: Host orders for each egg parasitoid genus and percentages
DOI: 10.6084/m9.figshare.12625808.v2
title: ESM table S2 from How to escape from insect egg parasitoids: a review of potential factors explaining parasitoid absence across the Insecta

description: Host orders for each egg parasitoid genus and percentages
DOI: 10.6084/m9.figshare.12625805.v2
title: ESM S1 from How to escape from insect egg parasitoids: a review of potential factors explaining parasitoid absence across the Insecta

description: Location of host eggs by parasitoids and information on most important egg parasitoid genera, incl. figure S1
DOI: 10.6084/m9.figshare.12625808.v1
title: ESM table S2 from How to escape from insect egg parasitoids: a review of potential factors explaining parasitoid absence across the insecta

description: Host orders for each egg parasitoid genus and percentages
DOI: 10.6084/m9.figshare.12625805.v1
title: ESM S1 from How to escape from insect egg parasitoids: a review of potential factors explaining parasitoid absence across the insecta

description: Location of host eggs by parasitoids and information on most important egg parasitoid genera, incl. figure S1
DOI: 10.6084/m9.figshare.12625790
title: Table S3 from Vertical structure in chlorophyll profiles: influence on primary production in the Arctic Ocean

description: Light absorption spectrum of Atlantic Arctic phytoplankton normalised to 440 nm used in the spectrally-resolved model of marine primary production.
DOI: 10.6084/m9.figshare.12625784
title: Table S1 from Vertical structure in chlorophyll profiles: influence on primary production in the Arctic Ocean

description: Summary of the chlorophyll profile parameters obtained by fitting the shifted Gaussian function to chlorophyll profile data. Information on research cruise (CRUISE), day number (DN), day of year (DAY), month of year (MONTH), year (YEAR), local time (TIME), latitude (LAT), longitude (LON), depth of the chlorophyll maximum (ZM), background chlorophyll concentration (B0), peak area (H), and width (SIGMA).
DOI: 10.6084/m9.figshare.12625790.v1
title: Table S3 from Vertical structure in chlorophyll profiles: influence on primary production in the Arctic Ocean

description: Light absorption spectrum of Atlantic Arctic phytoplankton normalised to 440 nm used in the spectrally-resolved model of marine primary production.
DOI: 10.6084/m9.figshare.12625776
title: Data files from Arctic coastal benthos long-term responses to perturbations under climate warming

description: Climate warming influences structure and function of Arctic benthic ecosystems. Assessing the response of these systems to perturbations requires long-term studies addressing key ecological processes related to recolonization and succession of species. Based on unique time-series (1980–2017), this study addresses successional patterns of hard-bottom benthos in two fjords in NW Svalbard after a pulse perturbation in 1980 and during a period of rapid climate warming. Analysis of seafloor photographs revealed different return rates of taxa, and variability in species densities, through time. It took 13 and 24 years for the community compositions of cleared and control transects to converge in the two fjords. Nearly two decades after the study initiation, an increase in filamentous and foliose macroalgae was observed with a subsequent reorganization in the invertebrate community. Trait analyses showed a decrease in body size and longevity of taxa in response to the pulse perturbation and a shift towards small/medium size and intermediate longevity following the macroalgae takeover. The observed slow recovery rates and abrupt shifts in community structure document the vulnerability of Arctic coastal ecosystems to perturbations and continued effects of climate warming.This article is part of the theme issue ‘The Changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystems’.
DOI: 10.6084/m9.figshare.12625781
title: Table S2 from Vertical structure in chlorophyll profiles: influence on primary production in the Arctic Ocean

description: Summary of the photosynthesis-irradiance parameters obtained by fitting the equation of Platt et al. [28] to 14C incubation experiments. Information on research cruise and location (CRUISEID), latitude (LAT), longitude (LON), depth (m), year (YEAR), month of year (MONTH), day of year (DAY), chlorophyll-a concentration (TCHL), initial slope (ALPHA), assimilation number (PMB).
DOI: 10.6084/m9.figshare.12625781.v1
title: Table S2 from Vertical structure in chlorophyll profiles: influence on primary production in the Arctic Ocean

description: Summary of the photosynthesis-irradiance parameters obtained by fitting the equation of Platt et al. [28] to 14C incubation experiments. Information on research cruise and location (CRUISEID), latitude (LAT), longitude (LON), depth (m), year (YEAR), month of year (MONTH), day of year (DAY), chlorophyll-a concentration (TCHL), initial slope (ALPHA), assimilation number (PMB).
DOI: 10.6084/m9.figshare.12625784.v1
title: Table S1 from Vertical structure in chlorophyll profiles: influence on primary production in the Arctic Ocean

description: Summary of the chlorophyll profile parameters obtained by fitting the shifted Gaussian function to chlorophyll profile data. Information on research cruise (CRUISE), day number (DN), day of year (DAY), month of year (MONTH), year (YEAR), local time (TIME), latitude (LAT), longitude (LON), depth of the chlorophyll maximum (ZM), background chlorophyll concentration (B0), peak area (H), and width (SIGMA).