cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.js88n
title: Data from: Estimating the duration of speciation from phylogenies

description: Speciation is not instantaneous but takes time. The protracted birth-death
 diversification model incorporates this fact and predicts the often
 observed slowdown of lineage accumulation towards the present. The
 mathematical complexity of the protracted speciation model has barred
 estimation of its parameters until recently a method to compute the
 likelihood of phylogenetic branching times under this model was outlined
 (Lambert et al. 2014). Here we implement this method and study using
 simulated phylogenies of extant species how well we can estimate the model
 parameters (rate of initiation of speciation, rate of extinction of
 incipient and good species, and rate of completion of speciation) as well
 as the duration of speciation, which is a combination of the
 aforementioned parameters. We illustrate our approach by applying it to a
 primate phylogeny. The simulations show that phylogenies often do not
 contain enough information to provide unbiased estimates of the
 speciation-initiation rate and the extinction rate, but the duration of
 speciation can be estimated without much bias. The estimate of the
 duration of speciation for the primate clade is consistent with literature
 estimates. We conclude that phylogenies combined with the protracted
 speciation model provides a promising way to estimate the duration of
 speciation.
description: Etienne et al -
 Evolution 2014 - supporting dataEtienne_et_al_-_Evolution_2014_-_supporting_data.zip
DOI: 10.5061/dryad.3sn4t
title: Data from: Systematic study of the surface plasmon resonance signals generated by cells for sensors with different characteristic lengths

description: The objectives of this study were to establish an in-depth understanding
 of the signals induced by mammalian cells in surface plasmon resonance
 (SPR) sensing. To this end, two plasmonic structures with different
 propagation and penetration distances were used: conventional surface
 plasmon resonance and long-range surface plasmon resonance. Long-range SPR
 showed a lesser sensitivity to the absolute number of round cells but a
 greater resolution due to its very narrow spectral dip. The effect of cell
 spreading was also investigated and the resonance angle of long-range SPR
 was mostly insensitive unlike in the conventional SPR counterpart.
 Experimental data was compared with suitable models used in the SPR
 literature. Although these simple averaging models could be used to
 describe some of the experimental data, important deviations were observed
 which could be related to the fact that they do not take into
 consideration critical parameters such as plasmon scattering losses, which
 is particularly crucial in the case of long-range SPR structures. The
 comparison between conventional and long-range SPR for cellular schemes
 revealed important fundamental differences in their responses to the
 presence of cells, opening new horizons for SPR-based cell assays. From
 this study, long-range SPR is expected to be more sensitive towards both
 the detection of intracellular events resulting from biological
 stimulation and the detection of microorganisms captured from complex
 biological samples.
description: all data - from
 micrographs to spectraPlease refer to the
 ReadMe file for more information.data.zip
DOI: 10.5061/dryad.p30c6
title: Data from: High-yielding corn response to applied phosphorus, potassium, and sulfur in Nebraska

description: Nutrient management recommendations may change as yield levels and
 efficiency of crop production increase. Recommendations for P, K, and S
 were evaluated using results from 34 irrigated corn (Zea mays L.) trials
 conducted in diverse situations across Nebraska. The mean yield was 14.7
 Mg ha−1 with adequate fertilizer applied. The median harvest index values
 were 0.52, 0.89, 0.15, and 0.56 for biomass, P, K, and S, respectively.
 Median grain yields were 372, 49, and 613 kg kg−1 of aboveground plant
 uptake of P, K, and S, respectively. The estimated critical Bray-1 P level
 for corn response to 20 kg P ha−1 was 20 mg kg−1 when the previous crop
 was corn compared with 10 mg kg−1 when corn followed soybean [Glycine max
 (L.) Merr.]. Soil test K was generally high with only three site-years
 &lt;125 mg kg−1 Over all trials, application of 40 kg K ha−1 resulted
 in a 0.2 Mg ha−1 mean grain yield decrease. Application of 22 kg S ha−1
 did not result in significant yield increase in any trial. Soil test
 results accounted for twice as much variation in nutrient uptake when soil
 organic matter (SOM) and pH were considered in addition to the soil test
 nutrient values. The results indicate a need to revise the current
 recommendation for P, to maintain the current K and S recommendations, and
 to use SOM and pH in addition to soil test nutrient values in estimating
 applied nutrient requirements for irrigated high yield corn production.
description: Nutrient response data
 for high yield corn in NebraskaThe file Nebr
 HiYieldCornNPKS contains data for 34 site-years of research for high yield
 corn response to applied nutrients in Nebraska. The mean highest treatment
 yield was 14.75 Mg ha-1.Nebr
 HiYieldCornNPKS.xls
DOI: 10.5061/dryad.73fq4
title: Data from: Binding space and time through action

description: Space and time are intimately coupled dimensions in the human brain.
 Several lines of evidence suggest that space and time are processed by a
 shared analogue magnitude system. It has been proposed that actions are
 instrumental in establishing this shared magnitude system. Here we provide
 evidence in support of this hypothesis, by showing that the interaction
 between space and time is enhanced when magnitude information is acquired
 through action. Participants observed increases or decreases in the height
 of a visual bar (spatial magnitude) while judging whether a simultaneously
 presented sequence of acoustic tones had accelerated or decelerated
 (temporal magnitude). In one condition (Action), participants directly
 controlled the changes in bar height with a hand grip device, whereas in
 the other (No Action), changes in bar height were externally controlled
 but matched the spatial/temporal profile of the Action condition. The sign
 of changes in bar height biased the perceived rate of the tone sequences,
 where increases in bar height produced apparent increases in tone rate.
 This effect was amplified when the visual bar was actively controlled in
 the Action condition, and the strength of the interaction was scaled by
 the magnitude of the action. Subsequent experiments ruled out that this
 was simply explained by attentional factors, and additionally showed that
 a monotonic mapping is also required between grip force and bar height in
 order to bias the perception of the tones. These data provide support for
 an instrumental role of action in interfacing spatial and temporal
 quantities in the brain.
description: raw_dataExperiment 1-6 raw & grip force data (MATLAB .mat files)
DOI: 10.5061/dryad.bv3nf
title: Data from: The excreted microbiota of bats: evidence of niche specialization based on multiple body habitats

description: Animal-associated microbiotas form complex communities, which play crucial
 functions for their host, including susceptibility to infections. Despite
 increasing attention to bats as reservoirs of zoonotic pathogens, their
 microbiota is poorly documented, especially for samples potentially
 implicated in pathogen transmission such as urine and saliva. Here, using
 low-biomass individual samples, we examined the composition and structure
 of bacterial communities excreted by insectivorous bats, focusing on three
 body habitats (saliva, urine and faeces). We show that niche
 specialisation occurs as bacterial community composition was distinct
 across body habitats with the majority of phylotypes being body habitat
 specific. Our results suggest that urine harbours more diverse bacterial
 communities than saliva and faeces and reveal potentially zoonotic
 bacteria such as Leptospira, Rickettsia, Bartonella and Coxiella in all
 body habitats. Our study emphasised that, in addition to the traditional
 use of gut-associated samples such as faeces, both urine and saliva are
 also of interest because of their diverse microbiota and the potential
 transmission of pathogenic bacteria. Our results represent a critical
 baseline for future studies investigating the interactions between
 microbiota and infection dynamics in bats.
description: Dietrich_Mothur_Phylotype_tableThis file contains the phylotype table of the 18 bat samples and 2 negative controls, after processing with MOTHUR.Dietrich_readsThis folder contains the FASTQ.GZ files with the 16S rRNA sequences generated for the 18 bat samples and the 2 negative controls. Forward and reverse primers were removed at 100% nucleotidic identity and sequences were quality trimmed when Q score &lt; 30.
DOI: 10.5061/dryad.ft7c7
title: Data from: Self-assembly behaviors of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism

description: Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique
 and specific features to build one-component nanomedicines. Supramolecular
 structure based on PDCs could form various morphologies ranging from
 nanotube, nanofiber, nanobelt to hydrogel. However, the assembly process
 of PDCs is too complex to predict or control. Herein, we investigated the
 effects of extrinsic factors on assembly morphology and the possible
 formation of nanostructures based on PCDs. To this end, we designed a PDC
 consisting of hydrophobic drug (S)-ketoprofen (Ket) and valine-glutamic
 acid dimeric repeats peptide (L-VEVE) to study their assembly behavior.
 Our results showed that the critical assembly concentration of Ket-L-VEVE
 was 0.32 mM in water to form various nanostructures which experienced from
 micelle, nanorod, nanofiber to nanoribbon. The morphology was influenced
 by multiple factors including molecular design, assembly time, pH and
 hydrogen bond inhibitor. On the basis of experimental results, we
 speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking
 interaction between Ket molecules could serve as an anchor, and hydrogen
 bonded induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE
 peptide play structure-directing role in forming filament-like or
 nanoribbon morphology. This work provides a new sight to rationally design
 and precisely control the nanostructure of PDCs based on aromatic
 fragment.
description: self-assembly
 reseachchen
 datas.zip
DOI: 10.5061/dryad.j9k60
title: Data from: Combined use of GPS and accelerometry reveals fine scale three-dimensional foraging behaviour in the short-tailed shearwater

description: Determining the foraging behaviour of free-ranging marine animals is
 fundamental for assessing their habitat use and how they may respond to
 changes in the environment. However, despite recent advances in
 bio-logging technology, collecting information on both at-sea movement
 patterns and activity budgets still remains difficult in small pelagic
 seabird species due to the constraints of instrument size. The
 short-tailed shearwater, the most abundant seabird species in Australia
 (ca 23 million individuals), is a highly pelagic procellariiform. Despite
 its ecological importance to the region, almost nothing is known about its
 at-sea behaviour, in particular, its foraging activity. Using a
 combination of GPS and tri-axial accelerometer data-loggers, the fine
 scale three-dimensional foraging behaviour of 10 breeding individuals from
 two colonies was investigated. Five at-sea behaviours were identified: (1)
 resting on water, (2) flapping flight, (3) gliding flight, (4) foraging
 (i.e., surface foraging and diving events), and (5) taking-off. There were
 substantial intra- and inter- individual variations in activity patterns,
 with individuals spending on average 45.8% (range: 17.1–70.0%) of time at
 sea resting on water and 18.2% (range: 2.3–49.6%) foraging. Individuals
 made 76.4 ± 65.3 dives (range: 8–237) per foraging trip (mean duration 9.0
 ± 1.9 s), with dives also recorded during night-time. With the continued
 miniaturisation of recording devices, the use of combined data-loggers
 could provide us with further insights into the foraging behaviour of
 small procellariiforms, helping to better understand interactions with
 their prey.
description: GPS tracking data and
 behavioural statesGPS tracking data and
 behavioural states of 10 breeding short-tailed shearwaters performing
 short foraging trips
DOI: 10.5061/dryad.50003
title: Data from: Spatiotemporal dynamic of surface water bodies using Landsat time-series data from 1999 to 2011

description: Detailed information on the spatiotemporal dynamic in surface water bodies
 is important for quantifying the effects of a drying climate, increased
 water abstraction and rapid urbanization on wetlands. The Swan Coastal
 Plain (SCP) with over 1500 wetlands is a global biodiversity hotspot
 located in the southwest of Western Australia, where more than 70% of the
 wetlands have been lost since European settlement. SCP is located in an
 area affected by recent climate change that also experiences rapid urban
 development and ground water abstraction. Landsat TM and ETM+ imagery from
 1999 to 2011 has been used to automatically derive a spatially and
 temporally explicit time-series of surface water body extent on the SCP. A
 mapping method based on the Landsat data and a decision tree
 classification algorithm is described. Two generic classifiers were
 derived for the Landsat 5 and Landsat 7 data. Several landscape metrics
 were computed to summarize the intra and interannual patterns of surface
 water dynamic. Top of the atmosphere (TOA) reflectance of band 5 followed
 by TOA reflectance of bands 4 and 3 were the explanatory variables most
 important for mapping surface water bodies. Accuracy assessment yielded an
 overall classification accuracy of 96%, with 89% producer’s accuracy and
 93% user’s accuracy of surface water bodies. The number, mean size, and
 total area of water bodies showed high seasonal variability with highest
 numbers in winter and lowest numbers in summer. The number of water bodies
 in winter increased until 2005 after which a decline can be noted. The
 lowest numbers occurred in 2010 which coincided with one of the years with
 the lowest rainfall in the area. Understanding the spatiotemporal dynamic
 of surface water bodies on the SCP constitutes the basis for understanding
 the effect of rainfall, water abstraction and urban development on water
 bodies in a spatially explicit way.
description: SCP_shapefiles
DOI: 10.5061/dryad.r0d1q
title: Data from: Matching oceanography and genetics at the basin scale. Seascape connectivity of the Mediterranean shore crab in the Adriatic Sea

description: Investigating the interactions between the physical environment and early
 life history is crucial to understand the mechanisms that shape the
 genetic structure of marine populations. Here, we assessed the genetic
 differentiation in a species with larval dispersal, the Mediterranean
 shore crab (Carcinus aestuarii) in the Adriatic Sea (central
 Mediterranean), and we investigated the role of oceanic circulation in
 shaping population structure. To this end, we screened 11 polymorphic
 microsatellite loci from 431 individuals collected at eight different
 sites. We found a weak, yet significant, genetic structure into three
 major clusters: a northern Adriatic group, a central Adriatic group, and
 one group including samples from southern Adriatic and Ionian seas.
 Genetic analyses were compared, under a seascape genetics approach, with
 estimates of potential larval connectivity obtained with a coupled
 physical-biological model that integrates a water circulation model and a
 description of biological traits affecting dispersal. The cross-validation
 of the results of the two approaches supported the view that genetic
 differentiation reflects an oceanographic subdivision of the Adriatic Sea
 into three sub-basins, with circulation patterns allowing the exchange of
 larvae through permanent connections linking north Adriatic sites and
 ephemeral connections like those linking the central Adriatic with
 northern and southern locations.
description: Caestuarii_genotypesMicrosatellite genotypes for 431 Carcinus aestuarii individuals from 8 population samples.Lagrangian_simulations_code&settingsCompressed archive (.zip) containing the source code and settings used for Lagrangian simulations.
DOI: 10.5061/dryad.cv20d
title: Data from: Range wide parallel climate-associated genomic clines in Atlantic salmon

description: Clinal variation across replicated environmental gradients can reveal
 evidence of local adaptation, providing insight into the demographic and
 evolutionary processes that shape intraspecific diversity. Using 1773
 genome-wide single nucleotide polymorphisms we evaluated latitudinal
 variation in allele frequency for 134 populations of North American and
 European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195
 (11%) loci showing clinal patterns in North America and Europe
 respectively, with 12 clinal loci in common between continents. Clinal
 SNPs were evenly distributed across the salmon genome and logistic
 regression revealed significant associations with latitude and seasonal
 temperatures, particularly average spring temperature in both continents.
 Loci displaying parallel clines were associated with several metabolic and
 immune functions, suggesting a potential basis for climate associated
 adaptive differentiation. These climate-based clines collectively suggest
 evidence of large scale environmental associated differences on either
 side of the North Atlantic. Our results support patterns of parallel
 evolution on both sides of the North Atlantic, with evidence of both
 similar and divergent underlying genetic architecture. The identification
 of climate associated genomic clines illuminates the role of selection and
 demographic processes on intraspecific diversity in this species and
 provides a context in which to evaluate the impacts of climate change.
description: Salmon_AllRivers_GenepopGenepop file of all European and North American rivers with 1773 loci.AllRivers_Oct2016_1773LociGP.txtGenepop files of clinal lociTwo genepop files with clinal loci from North American and European rivers.ClinalLoci_GP.zipEnvironmental DataEnvironmental data used in our study for climate associations with genetic clustering coefficients.EnvironmentalData.zipR_scriptsR scripts for selecting clinal loci based on our criteria and replicating our analyses looking at structure and climate associations.
DOI: 10.5061/dryad.nm70b
title: Data from: Subtype diversity and reassortment potential for co-circulating avian influenza viruses at a diversity hot spot

description: 1. Biological diversity has long been used to measure ecological health.
 While evidence exists from many ecosystems that declines in host
 biodiversity may lead to greater risk of disease emergence, the role of
 pathogen diversity in the emergence process remains poorly understood.
 Particularly, because a more diverse pool of pathogen types provides more
 ways in which evolutionary innovations may arise, we suggest that
 host–pathogen systems with high pathogen diversity are more prone to
 disease emergence than systems with relatively homogeneous pathogen
 communities. We call this prediction the diversity-emergence hypothesis.
 2. To show how this hypothesis could be tested, we studied a system
 comprised of North American shorebirds and their associated
 low-pathogenicity avian influenza (LPAI) viruses. These viruses are
 important as a potential source of genetic innovations in influenza. A
 theoretical contribution of this study is an expression predicting the
 rate of viral subtype reassortment to be proportional to both prevalence
 and Simpson's Index, a formula that has been used traditionally to
 quantify biodiversity. We then estimated prevalence and subtype diversity
 in host species at Delaware Bay, a North American AIV hotspot, and used
 our model to extrapolate from these data. 3. We estimated that 4 to 39
 virus subtypes circulated at Delaware Bay each year between 2000 and 2008,
 and that surveillance coverage (percentage of co-circulating subtypes
 collected) at Delaware Bay is only about 63·0%. Simpson's Index in
 the same period varied more than fourfold from 0·22 to 0·93. These
 measurements together with the model provide an indirect, model-based
 estimate of the reassortment rate. A proper test of the
 diversity-emergence hypothesis would require these results to be joined to
 independent and reliable estimates of reassortment, perhaps obtained
 through molecular surveillance. 4. These results suggest both that subtype
 diversity (and therefore reassortment) varies from year to year and that
 several subtypes contributing to reassortment are going undetected. The
 similarity between these results and more detailed studies of one host,
 ruddy turnstone (Arenaria interpres), further suggests that this species
 may be the primary host for influenza reassortment at Delaware Bay. 5.
 Biological diversity has long been quantified using Simpson's Index.
 Our model links this formula to a mechanistic account of reassortment in
 multipathogen systems in the form of subtype diversity at Delaware Bay,
 USA. As a theory of how pathogen diversity may influence the evolution of
 novel pathogens, this work is a contribution to the larger project of
 understanding the connections between biodiversity and disease.
description: barton-jae-dataData contains raw data (comma separated values and a GIS shapefile) and R code for producing the analyses and figures in the associated paper.
DOI: 10.5061/dryad.8g7h7
title: Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs

description: Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial
 (anterior) cruciate ligament (RCCL) are the most common complex orthopedic
 traits of dogs and all result in debilitating osteoarthritis. Herein we
 reanalyzed previously reported data: the Norberg angle (a quantitative
 measure of HD) in 921 dogs, ED in 113 cases and 633 controls, and RCCL in
 271 cases and 399 controls and their genotypes at ~185,000 single
 nucleotide polymorphisms. A novel fixed and random model with a
 circulating probability unification (FarmCPU) function, with marker-based
 principal components and a kinship matrix to correct for population
 stratification, was used. A Bonferroni correction at p&lt;0.01
 resulted in a pgenome of 6.96 ×10-8. Six loci were identified; three for
 HD and three for RCCL. An associated locus at CFA28:34,369,342 for HD was
 described in the same dogs using a conventional mixed model. No loci were
 identified for RCCL in the previous report but the two loci for ED in the
 previous report did not reach genome-wide significance using the FarmCPU
 model. These results were supported by simulation which demonstrated that
 the FarmCPU held no power advantage over the linear mixed model for the ED
 sample but provided additional power for the HD and RCCL samples.
 Candidate genes for HD and RCCL are discussed. When using FarmCPU
 software, we recommend a resampling test, that a positive control be used
 to determine the optimum pseudo quantitative trait nucleotide-based
 covariate structure of the model, and a negative control be used
 consisting of permutation testing and the identical resampling test as for
 the non-permuted phenotypes.
description: RCCL
 .bedrccl.bed.gzRCCL .famrccl.fam.gzRCCL .bimrccl.bim.gzHD .bedHD.bed.gzHD .bimHD.bim.gzHD .famHD.fam.gzED .famED.fam.gzED .bedED.bed.gzED .bimED.bim.gz