cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.26767
title: Data from: Modelling the evolution of HIV-1 virulence in response to imperfect therapy and prophylaxis

description: Average HIV-1 virulence appears to have evolved in different directions in
 different host populations since antiretro- viral therapy first became
 available, and models predict that HIV drugs can select for either higher
 or lower virulence, depending on how treatment is administered. However,
 HIV virulence evolution in response to ‘leaky’ therapy (treat- ment that
 imperfectly suppresses viral replication) and the use of preventive drugs
 (pre-exposure prophylaxis) has not been explored. Using adaptive dynamics,
 we show that higher virulence can evolve when antiretroviral therapy is
 im- perfectly effective, and that this evolution erodes some of the
 long-term clinical and epidemiological benefits of HIV treatment. The
 introduction of pre-exposure prophylaxis greatly reduces infection
 prevalence, but can further amplify virulence evolution when it, too, is
 leaky. Increasing the uptake rate of these imperfect interventions
 increases selection for higher virulence, and can lead to counterintuitive
 increases in infection prevalence in some scenarios. Although populations
 almost always fare better with access to interventions than without,
 untreated individuals could experi- ence particularly poor clinical
 outcomes when virulence evolves. These findings predict that
 antiretroviral drugs may have underappreciated evolutionary consequences,
 but that maximizing drug efficacy can prevent this evolutionary response.
 We suggest that HIV virulence evolution should be closely monitored as
 access to interventions continues to improve.
description: Mathematica
 codeA
 Mathematica notebook containing and describing the code used for all
 numerical analyses in this publication. Also included is the code used to
 generate all figures, both in the main text and supporting
 information.SmithMideo2017.nb
DOI: 10.5061/dryad.58416
title: Data from: What kind of maternal effects can be selected for in fluctuating environments?

description: Just as phenotypic plasticity can evolve when developing individuals get
 informational cues about their future adult environment, deterministic
 maternal effects, where offspring trait values depend on the maternal
 environment, can evolve when mothers gain reliable information about the
 environments their offspring will face. Randomizing maternal effects (a
 type of diversifying bet hedging), where offspring trait values are
 randomized, can evolve by natural selection even when information about
 future environments is unavailable. We investigate selection on both
 randomizing and deterministic maternal effects in environments that show
 correlated fluctuations between two environmental states. We compare the
 strength of selection for deterministic and randomizing maternal effects
 and explicitly consider maternal fitness costs of producing offspring with
 different phenotypes. Only a small set of environmental parameters allow
 randomizing maternal effects to outcompete deterministic maternal effects;
 not only must there be little or no information available about future
 environments, but the frequency of each environment must fall within a
 narrow range. By contrast, deterministic maternal effects can always
 invade an ancestral state lacking a maternal effect even if the amount of
 environmental information available is low. The long-term outcome may
 involve offspring trait value randomization but only if trait values first
 evolve to cause extreme differences in environment-specific fitness.
 Overall, deterministic maternal effects are more likely to evolve by
 natural selection than randomizing maternal effects.
description: SimulationCodeCode to run single population simulations and plot the results.ConditionalSimThis is a Mathematica package file that can be read or input into Mathematica. It contains a simulation function that runs a single population simulation until a preset terminating condition is met.ExampleSimulationCallThis is a plain text file that contains a script for running a set of simulations in Mathematica.
DOI: 10.6084/m9.figshare.31157651
title: Fasta file representing the alignment of human, rat and mouse aa sequences of IP3R1, IP3R2 and IP3R3 from Anti-apoptotic BCL-2 binds to all three IP3R isoforms, thereby limiting the Ca2+-flux properties of IP3R homo-tetramers

description: Alignment of all 9 evaluated IP3R sequences.fa
DOI: 10.6084/m9.figshare.31157651.v1
title: Fasta file representing the alignment of human, rat and mouse aa sequences of IP3R1, IP3R2 and IP3R3 from Anti-apoptotic BCL-2 binds to all three IP3R isoforms, thereby limiting the Ca2+-flux properties of IP3R homo-tetramers

description: Alignment of all 9 evaluated IP3R sequences.fa
DOI: 10.5061/dryad.gr1pk
title: Data from: Trpc2 Pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss

description: Comparative methods are often used to infer loss or gain of complex
 phenotypes, but few studies take advantage of genes tightly linked with
 complex traits to test for shifts in the strength of selection. In mammals
 vomerolfaction detects chemical cues mediating many social and
 reproductive behaviors and is highly conserved, but all bats exhibit
 degraded vomeronasal structures with the exception of two families
 (Phyllostomidae and Miniopteridae). These families either regained
 vomerolfaction after ancestral loss, or there were many independent losses
 after diversification from an ancestor with functional vomerolfaction. In
 this study, we use the Transient receptor potential cation channel 2
 (Trpc2) as a molecular marker for testing the evolutionary mechanisms of
 loss and gain of the mammalian vomeronasal system. We sequenced Trpc2 exon
 2 in over 100 bat species across 17 of 20 chiropteran families. Most
 families showed independent pseudogenizing mutations in Trpc2, but the
 reading frame was highly conserved in phyllostomids and miniopterids.
 Phylogeny-based simulations suggest loss of function occurred after bat
 families diverged, and purifying selection in two families has persisted
 since bats shared a common ancestor. As most bats still display
 pheromone-mediated behavior, they might detect pheromones through the main
 olfactory system without using the Trpc2 signaling mechanism.
description: for_DryadThis file contains controls files and output for gene tree inference (Garli), control files for evolver simulations (evolver), control files, input files, and output for both PAML (PAML_codeml) and RELAX analyses (RELAX), and R code to make Figures 4 and 5.
DOI: 10.5061/dryad.7n82c
title: Data from: Macroevolutionary synthesis of flowering plant sexual systems

description: Sexual system is a key determinant of genetic variation and reproductive
 success, affecting evolution within populations and within clades. Much
 research in plants has focused on evolutionary transitions away from the
 most common state of hermaphroditism and toward the rare state of dioecy
 (separate sexes). Rather than transitions predominantly toward greater
 sexual differentiation, however, evolution may proceed in the direction of
 lesser sexual differentiation. We analyzed the macroevolutionary dynamics
 of sexual system in angiosperm genera that contain both dioecious and
 non-dioecious species. Our phylogenetic analyses encompass a total of 2145
 species from 40 genera. Overall, we found little evidence that rates of
 sexual system transitions are greater in any direction. Counting the
 number of inferred state changes revealed a mild prevalence of transitions
 away from hermaphroditism and away from dioecy, toward states of
 intermediate sexual differentiation. We identify genera in which future
 studies of sexual system evolution might be especially productive, and we
 discuss how integrating genetic or population-level studies of sexual
 system could improve the power of phylogenetic comparative analyses. Our
 work adds to the evidence that different selective pressures and
 constraints act in different groups, helping maintain the variety of
 sexual systems observed among plants.
description: Data and
 analysesPhylogenetic trees.
 Sexual system tip states. Scripts to fit macroevolutionary models. Scripts
 to generate figures. Other visual summaries of data and
 results.DioecyDataAnalyses.tar.gz
DOI: 10.5061/dryad.b331s
title: Data from: Dianyuea gen. nov. (Salicaceae: Scyphostegioideae) from southwestern China

description: Dianyuea C. Shang, S. Liao & Z. X. Zhang, a new monotypic genus of
 Salicaceae based on Flacourtia turbinata H. J. Dong & H. Peng, is
 described and illustrated. Morphologically, Dianyuea differs from
 Flacourtia Comm. ex L'Hér. by having six connate stamens, basal
 placentation and lobed seed appendages. All those features indicate that
 Dianyuea is allied with Scyphostegia Stapf. A molecular phylogenetic
 analysis using plastid trnL-F, matK, and rbcL sequence data for
 representatives of 16 genera in Salicaceae s.l. shows that Dianyuea is
 sister to Scyphostegia. The new combination Dianyuea turbinata (H. J. Dong
 & H. Peng) C. Shang, S. Liao & Z. X. Zhang is proposed.
description: Dianyuea
 turbinata_matKDianyuea turbinata
 maturase K (matK) gene, partial cds; chloroplastDianyuea
 turbinata_rbcLDianyuea turbinata
 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene,
 partial cds; chloroplastDianyuea
 turbinata_trnH-LDianyuea turbinata
 trnL-trnF intergenic spacer, partial sequence;
 chloroplastMATK-F.1392427.C05MatK original sequence data, forwardMATK-R.1392428.C06MatK original sequence data, reverseRBCL-F.1392429.C07rbcL original sequence data, forwardRBCL-R.1392430.C08MatK original sequence data, reverseTRNL-F.YP01513957.E05trnL-trnF original sequence data, forwardTRNL-R.YP01513958.E06trnL-trnF original sequence data, reverse
DOI: 10.5281/zenodo.18386471
title: Global lake organic carbon burial dataset

description: see README.txt
DOI: 10.15468/dl.5ye5kv
title: Occurrence Download

description: A dataset containing 705370 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Meise Botanic Garden Herbarium (BR)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 705370 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001482-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.66gd7
title: Data from: Green approach for synthesis of bioactive Hantzsch 1,4-dihydropyridine derivatives based on thiophene moiety via multicomponent reaction

description: A novel green and efficient one-pot multicomponent reaction of
 dihydropyridine derivatives was reported as having good to excellent
 yield. In the presence of the catalyst ceric ammonium nitrate (CAN),
 different 1,3-diones and same starting materials as
 5-bromothiophene-2-carboxaldehyde and ammonium acetate were used at room
 temperature under solvent-free condition for the Hantzsch pyridine
 synthesis within a short period of time. All compounds were evaluated for
 their in vitro antibacterial and antifungal activity and, interestingly,
 we found that 5(b–f) show excellent activity compared with Ampicillin,
 whereas only the 5e compound shows excellent antifungal activity against
 Candida albicans compared with griseofulvin. The cytotoxicity of all
 compounds has been assessed against breast tumour cell lines (BT-549), but
 no activity was found. The X-ray structure of one such compound, 5a,
 viewed as a colourless block crystal, corresponded accurately to a
 primitive monoclinic cell.
description: Supplementary Material
 for RSC Open Science 03.1.2017CrystalStructureReflection List
DOI: 10.5281/zenodo.18386470
title: Global lake organic carbon burial dataset

description: see README.txt
DOI: 10.5061/dryad.15358
title: Data from: Assessing the anti-fungal efficiency of filters coated with zinc oxide nanoparticles

description: Air filters support fungal growth, leading to generation of conidia and
 volatile organic compounds, causing allergies, infections and food
 spoilage. Filters that inhibit fungi are therefore necessary. Zinc oxide
 (ZnO) nanoparticles have anti-fungal properties and therefore are good
 candidates for inhibiting growth. Two concentrations (0.012 M and 0.12 M)
 were used to coat two types of filters (melt-blown and needle-punched) for
 three different periods (0.5, 5 and 50 min). Rhizopus stolonifer and
 Penicillium expansum isolated from spoiled pears were used as test
 organisms. Conidial suspensions of 105 to 103 spores ml−1 were prepared in
 Sabouraud dextrose agar at 50°C, and a modified slide-culture technique
 was used to test the anti-fungal properties of the filters. Penicillium
 expansum was the more sensitive organism, with inhibition at 0.012 M at
 only 0.5 min coating time on the needle-punched filter. The longer the
 coating time, the more effective inhibition was for both organisms.
 Furthermore, it was also determined that the coating process had only a
 slight effect on the Young's Moduli of the needle-punched filters,
 while the Young's Moduli of the melt-blown filters is more
 susceptible to the coating method. This work contributes to the assessment
 of the efficacy of filter coating with ZnO nanopaticles aimed at
 inhibiting fungal growth.
description: supplementary
 information_FINAL
DOI: 10.5061/dryad.6ck7g
title: Data from: Early mortality saves energy: estimating the energetic cost of excess offspring in a seabird

description: Offspring are often produced in excess as insurance against stochastic
 events or unpredictable resources. This strategy may result in high
 early-life mortality, yet age-specific mortality before offspring
 independence and its associated costs have rarely been quantified. In this
 study, we modelled age-specific survival from hatching to fledging using
 24 years of data on hatching order (HO), growth and age of mortality of
 more than 15 000 common tern (Sterna hirundo) chicks. We found that
 mortality peaked directly after hatching, after which it declined rapidly.
 Mortality hazard was best described with the Gompertz function, and was
 higher with later HO, mainly due to differences in baseline mortality
 hazard, rather than age-dependent mortality. Based on allometric
 mass–metabolism relationships and detailed growth curves of starving
 chicks, we estimated that the average metabolizable energy intake of
 non-fledged chicks was only 8.7% of the metabolizable energy intake of
 successful chicks during the nestling phase. Although 54% of hatchlings
 did not fledge, our estimates suggest them to have consumed only 9.3% of
 the total energy consumption of all hatched chicks in the population
 before fledging. We suggest that rapid mortality of excess offspring is
 part of an adaptive brood reduction strategy to the benefit of the
 parents.
description: Raw data chick survival
 and growth (1992-2015)Data on common tern
 chick survival and mass growth between 1992 and 2015 collected in the
 Bantersee research colony in Wilhelmshaven, Germany.
DOI: 10.5061/dryad.85tj6
title: Data from: Patterns of pollen and nectar foraging specialization by bumblebees over multiple timescales using RFID

description: The ecological success of social insects is frequently ascribed to
 improvements in task performance due to division of labour amongst
 workers. While much research has focused on improvements associated with
 lifetime task specialization, members of colonies can specialize on a
 given task over shorter time periods. Eusocial bees in particular must
 collect pollen and nectar rewards to survive, but most workers appear to
 mix collection of both rewards over their lifetimes. We asked whether
 bumblebees specialize over timescales shorter than their lifetime. We also
 explored factors that govern such patterns, and asked whether reward
 specialists made more foraging bouts than generalists. In particular, we
 described antennal morphology and size of all foragers in a single colony
 and related these factors to each forager’s complete foraging history,
 obtained using radio frequency identification (RFID). Only a small
 proportion of foragers were lifetime specialists; nevertheless,
 &gt;50% of foragers specialized daily on a given reward. Contrary to
 expectations, daily and lifetime reward specialists were not better
 foragers (being neither larger nor making more bouts); larger bees with
 more antennal olfactory sensilla made more bouts, but were not more
 specialized. We discuss causes and functions of short and long-term
 patterns of specialization for bumblebee colonies.
description: Raw XML RFID
 outputRaw XML output from the
 automated RFID system. Data processed according to the methods described
 in the publication is available upon request.RFID_xml.zip
DOI: 10.5061/dryad.m68q0
title: Data from: Elasticity improves handgrip performance and user experience during visuomotor control

description: Passive rehabilitation devices, providing motivation and feedback,
 potentially offer an automated and low-cost therapy method, and can be
 used as simple human–machine interfaces. Here, we ask whether there is any
 advantage for a hand-training device to be elastic, as opposed to rigid,
 in terms of performance and preference. To address this question, we have
 developed a highly sensitive and portable digital handgrip, promoting
 independent and repetitive rehabilitation of grasp function based around a
 novel elastic force and position sensing structure. A usability study was
 performed on 66 healthy subjects to assess the effect of elastic versus
 rigid handgrip control during various visuomotor tracking tasks. The
 results indicate that, for tasks relying either on feedforward or on
 feedback control, novice users perform significantly better with the
 elastic handgrip, compared with the rigid equivalent (11% relative
 improvement, 9–14% mean range; p &lt; 0.01). Furthermore, there was a
 threefold increase in the number of subjects who preferred elastic
 compared with rigid handgrip interaction. Our results suggest that device
 compliance is an important design consideration for grip training devices.
description: MMace CVR study
 dataTwo folders pertaining
 to the feedforward and feedback experiments. Each contains subfolders
 separating subjects and different tasks. The raw data is given in
 human-readable text files. Also included is an excel file with collated
 data from the questionnaires.
DOI: 10.5061/dryad.2jn03
title: Data from: The flashlight fish Anomalops katoptron uses bioluminescent light to detect prey in the dark

description: Bioluminescence is a fascinating phenomenon occurring in numerous animal
 taxa in the ocean. The reef dwelling splitfin flashlight fish (Anomalops
 katoptron) can be found in large schools during moonless nights in the
 shallow water of coral reefs and in the open surrounding water. Anomalops
 katoptron produce striking blink patterns with symbiotic bacteria in their
 sub-ocular light organs. We examined the blink frequency in A. katoptron
 under various laboratory conditions. During the night A. katoptron swims
 in schools roughly parallel to their conspecifics and display high blink
 frequencies of approximately 90 blinks/minute with equal on and off times.
 However, when planktonic prey was detected in the experimental tank, the
 open time increased compared to open times in the absence of prey and the
 frequency decreased to 20% compared to blink frequency at night in the
 absence of planktonic prey. During the day when the school is in a cave in
 the reef tank the blink frequency decreases to approximately 9
 blinks/minute with increasing off-times of the light organ. Surprisingly
 the non-luminescent A. katoptron with non-functional light organs
 displayed the same blink frequencies and light organ open/closed times
 during the night and day as their luminescent conspecifics. In the
 presence of plankton non-luminescent specimens showed no change in the
 blink frequency and open/closed times compared to luminescent A.
 katoptron. Our experiments performed in a coral reef tank show that A.
 katoptron use bioluminescent illumination to detect planktonic prey and
 that the blink frequency of A. katoptron light organs follow an exogenous
 control by the ambient light.
description: Blink behaviour,
 wavelength and anatomy dataset for Anomalops katoptron
DOI: 10.5061/dryad.m7589
title: Data from: Hummingbird pollination and the diversification of angiosperms: an old and successful association in Gesneriaceae

description: The effects of specific functional groups of pollinators in the
 diversification of angiosperms are still to be elucidated. We investigated
 whether the pollination shifts or the specific association with
 hummingbirds affected the diversification of a highly diverse angiosperm
 lineage in the Neotropics. We reconstructed a phylogeny of 583 species
 from the Gesneriaceae family and detected diversification shifts through
 time, inferred the timing and amount of transitions among pollinator
 functional groups, and tested the association between hummingbird
 pollination and speciation and extinction rates. We identified a high
 frequency of pollinator transitions, including reversals to
 insect-pollination. Diversification rates of the group increased through
 time since 25 Mya, coinciding with the evolution of hummingbird-like
 flowers and the arrival of hummingbirds in South America. We showed that
 plants pollinated by hummingbirds have a two-fold higher speciation rate
 compared to plants pollinated by insects, and that transitions among
 functional groups of pollinators had a little impact on the
 diversification process. We demonstrated that floral specialization on
 hummingbirds for pollination has triggered rapid diversification in the
 Gesneriaceae family since the early Miocene, and that it represents one of
 the oldest identified plant-hummingbird associations. Biotic drivers of
 plant diversification in the Neotropics could be more related to this
 specific type of pollinator (hummingbirds), than to shifts among different
 functional groups of pollinators.
description: Gesnerioideae Bayesian
 Common Ancestor treeGesne_Ago8_simple_combined_CA.treGesneriaceae_sample_treesThis file contains 200 posterior treesGesne_ago8_comb_200.treGesnerioideae Concatenated genescharset gene_ITS = 1-617 charset gene_matK = 618-1615 charset gene_rps16 = 1616-2765 charset gene_trnL = 2766-3813Gesne_concatenated_genes.phyTable S1Specimen voucher information, Genbank accession numbers, and inferred pollination statesSupp_TableS1_Voucher_table.xls