cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6076/d18c7v
title: Reinforcement learning links spontaneous dopamine transients to reward

description: In their pioneering study on dopamine release, Romo and Schultz speculated
 "... that the amount of dopamine released by unmodulated spontaneous
 impulse activity exerts a tonic, permissive influence on neuronal
 processes more actively engaged in preparation of self-initiated
 movements, ...". Motivated by the suggestion of
 "spontaneous impulses", we asked two questions. First, are there
 spontaneous impulses of dopamine that are released in cortex? This
 possibility is further motivated by the "ramp up" of
 dopaminergic neuronal activity that occurs when rodents navigate to a
 reward. Using cell-based optical sensors of extrasynaptic
 dopamine, [DA]ex, we found that spontaneous dopamine impulses in
 cortex of naive mice occur at a rate of ~ 0.01 per second.
 Next, can mice be trained to change the amplitude and/or timing
 of dopamine events triggered by internal brain dynamics, much as they can
 change the amplitude and timing of dopamine impulses based on an external
 cue? Using a reinforcement learning paradigm based solely on
 rewards that were gated by feedback from real-time measurements of [DA]ex,
 we found that mice can volitionally modulate their spontaneous [DA]ex. In
 particular, by only the second session of daily, hour-long training, mice
 increased the rate of impulses of [DA]ex, increased the amplitude of the
 impulses, and increased their tonic level of [DA]ex for a reward.
 Critically, mice learned to reliably elicit [DA]ex impulses prior to
 receiving a reward. These effects reversed when the reward was removed. We
 posit that spontaneous dopamine impulses may serve as a salient cognitive
 event in behavioral planning.
description: Imaging data was collected using two photon scanning microscopy
 (2PLSM). The CNiFER FRET response was calculated by drawing an ROI in each
 frame corresponding to the CNiFER injection site and averaging the
 intensity over this ROI. Behavioral data was collected from analog inputs
 to an ADInstruments PowerLab device. Running speed was calculated from the
 rotary encoder counts by taking a moving average of the counts over 1s
 windows centered around each collected datapoint. Licking rate was
 calculated from the optical lickometer signal by thresholding the
 intensity to generate a lick count. This was then converted to a licking
 rate using a moving average over 1s windows, as with running
 data. 
description: The dataset requires MATLAB to load, and is stored as a structure
 array. A readme file ("README.txt") has been uploaded as well,
 which documents the various fields within the structure array and how they
 correspond to the data taken.
DOI: 10.5061/dryad.rbnzs7hbr
title: Male age alone predicts paternity success under sperm competition when effects of age and past mating effort are experimentally separated

description: Older males often perform poorly under post-copulatory sexual selection.
 It is unclear, however, whether reproductive senescence is due to male age
 itself or the accumulated costs of the higher lifetime mating effort that
 is usually associated with male age. To date, very few studies have
 accounted for mating history and sperm storage when testing the effect of
 male age on sperm traits, and none test how age and past mating history
 influence paternity success under sperm competition. Here, we
 experimentally manipulate male mating history to tease apart its effects
 from that of age on ejaculate traits and paternity in the mosquitofish,
 Gambusia holbrooki. We found that old, naive males had more sperm
 than old, experienced males, while the reverse was true for young males.
 In contrast, neither male age nor mating history affected sperm velocity.
 Finally, using artificial insemination to experimentally control the
 number of sperm per male, we found that old males sired significantly more
 offspring than young males independently of their mating history. Our
 results highlight that the general pattern of male reproductive senescence
 described in many taxa may often be affected by two naturally confounding
 factors, male mating history and sperm age, rather than male age itself.
DOI: 10.5061/dryad.4b8gthtcq
title: A global ecological signal of extinction risk in terrestrial vertebrates

description: To determine the distribution and causes of extinction threat across
 functional groups of terrestrial vertebrates, we assembled a dataset on
 ecological traits for 18,016 species and tested, using phylogenetic
 comparative methods, which categories of habitat association, mode of
 locomotion, and feeding mode best predict extinction risk. We found that
 cave-dwelling amphibians, brachiating mammals (all of which are primates),
 aerial and scavenging birds, and pedal squamates are all
 disproportionately threatened with extinction. Across four vertebrate
 classes, agriculture, followed by logging, and then invasive species and
 disease are the most common risk factors of extinction. The most
 endangered species show simultaneous risk from multiple threat types. The
 disproportionate loss of species with certain functional traits, combined
 with increasing anthropogenic pressures, is likely to disrupt ecosystem
 functions globally if left unabated. A shift in focus from species- to
 trait-centric conservation practices will allow for the protection of
 at-risk functional diversity from regional to global scales.
DOI: 10.5061/dryad.sj3tx9659
title: A new species of Eranthemum L. (Acanthaceae) from Thailand and Laos

description: During preparation of a revision of the genus Eranthemum (Acanthaceae), it
 became evident that nine specimens from eastern and south-eastern
 floristic regions of Thailand and southern Laos, represent a new species,
 that is herein described, illustrated and given the name, E. decumbens.
 The new species has affinities to E. strictum and E. roseum. A key to the
 species occurring in Thailand is provided, together with ecological data,
 distribution map and conservation status.
description: The study is based on careful examination of morphological
 characters on specimens from the Thai herbaria BK, BKF, CMUB and QBG. In
 addition, images of herbarium specimens were examined from P. The
 taxonomic literature of the genus Eranthemum of various countries in Asia
 including India (Roxburgh 1820, Miquel 1858, Clarke 1885), Bhutan (Wood
 1994, 2001), China (Hu  et  al. 2011), Myanmar (Kress  et  al. 2003),
 Thailand (Imlay 1938, 1939, Hansen 1985, Charoenchai 2014, The Forest
 Herbarium, Royal Forest Dept 2014), Laos (Newman et al. 2007) and
 Indo-China (Benoist 1935) was consulted. A detailed description and line
 drawing were prepared based on herbarium specimen observations. The
 distribution, habitat and phenology were recorded from the specimen
 labels. The IUCN red list assessments were performed based on the extent
 of occurrence (EOO) and the area of occupancy (AOO) in the program R ver.
 3.5.1 (www.r-project.org).
DOI: 10.15468/dl.q7pbf9
title: Occurrence Download

description: A dataset containing 3280 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Balanidae, Serpulidae, Watersiporidae, Styelidae, Pennariidae, Mytilidae, Teredinidae, Ulvaceae, Caulerpaceae, Bougainvilliidae, Syllidae, Hydractiniidae, Varunidae, Bolinopsidae)",
 "Geometry POLYGON ((33.925781 30.297018, 30.849609 30.221102, 36.738281 17.978733, 42.539063 11.867351, 46.054688 9.362353000000001, 53.613281 12.297068, 64.6875 21.616579, 66.269531 25.403585, 65.302734 29.993002, 50.976563 32.398516, 33.925781 30.297018))"
 ]
}

 The dataset includes 3280 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002867-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gxd2547mc
title: Data from: Clathrin-independent endocytic retrieval of SV proteins mediated by the clathrin adaptor AP-2 at mammalian central synapses

description: Neurotransmission is based on the exocytic fusion of synaptic vesicles
 (SVs) followed by endocytic membrane retrieval and the reformation of SVs.
 Conflicting models have been proposed regarding the mechanisms of SV
 endocytosis, most notably clathrin/ AP-2-mediated endocytosis and
 clathrin-independent ultrafast endocytosis. Partitioning between these
 pathways has been suggested to be controlled by temperature and stimulus
 paradigm. We report on the comprehensive survey of six major SV proteins
 to show that SV endocytosis in mouse hippocampal neurons at physiological
 temperature occurs independent of clathrin while the endocytic retrieval
 of a subset of SV proteins including the vesicular transporters for
 glutamate and GABA depend on sorting by the clathrin adaptor AP-2. Our
 findings highlight a clathrin-independent role of the clathrin adaptor
 AP-2 in the endocytic retrieval of select SV cargos from the presynaptic
 cell surface and suggest a revised model for the endocytosis of SV
 membranes at mammalian central synapses.
DOI: 10.5061/dryad.xgxd254gv
title: Great tits (Parus major) flexibly learn that herbivore-induced plant volatiles indicate prey location – an experimental evidence with two tree species

description: 1. When searching for food, great tits (Parus major) can use
 herbivore-induced plant volatiles (HIPVs) as an indicator of arthropod
 presence. Their ability to detect HIPVs was shown to be learned, and not
 innate, yet the flexibility and generalization of learning remains
 unclear. 2. We studied if, and if so how, naïve and trained great tits
 (Parus major) discriminate between herbivore-induced and non-induced
 saplings of Scotch elm (Ulmus glabra) and cattley guava (Psidium
 cattleyanum). We chemically analysed the used plants and showed that their
 HIPVs differed significantly and overlapped only in a few compounds. 3.
 Birds trained to discriminate between herbivore-induced and non-induced
 saplings preferred the herbivore-induced saplings of the plant species
 they were trained to. Naïve birds did not show any preferences. Our
 results indicate that the attraction of great tits to herbivore-induced
 plants is not innate, rather it is a skill that can be acquired through
 learning, one tree species at a time. 4. We demonstrate that the ability
 to learn to associate HIPVs with food reward is flexible, expressed to
 both tested plant species, even if the plant species has not coevolved
 with the bird species (i.e. guava). Our results imply that the birds are
 not capable of generalising HIPVs among tree species but suggest that they
 either learn to detect individual compounds or associate whole bouquets
 with food rewards.
description: Birds were split into three groups. Two groups were trained to
 respective smells  or kept naive (Trained to: Psidium, Ulmus,
 Control). Bird = ID of the bird and each bird entered
 severa pair-wise tests in which it was suppose to search on trees
 familiar/unfamiliar to it and trees either chemicall induced or
 non-induced. The "induced psidium or induced ulmus " were
 considered as a focal tree, to which the data were related. The type of
 the tree on the other side of the cage was used as an explanatory factor
 and is noted in column "Other side". Measured
 variable were TimeClose = number of seconds spent in the proximity of the
 tree, TimeOn - time spent onthe tree by real searching for prey, these two
 variables were then related to the total length of the time spent 
 (TotalTimeCloseTree, TotalTimeOnTree) at any of the offered tree. THe
 values were expressed as bonamial (Binom) or in percentages
 (perc). Experiments were run at two cages, their
 nick-names are "wooden" and "metal".
DOI: 10.5061/dryad.7wm37pvt0
title: Distinct synaptic transfer functions in same-type photoreceptors

description: Many sensory systems use ribbon-type synapses to transmit their signals to
 downstream circuits. The properties of this synaptic transfer
 fundamentally dictate which aspects in the original stimulus will be
 accentuated or suppressed, thereby partially defining the detection limits
 of the circuit. Accordingly, sensory neurons have evolved a wide variety
 of ribbon geometries and vesicle pool properties to best support their
 diverse functional requirements. However, the need for diverse synaptic
 functions does not only arise across neuron types, but also within. Here
 we show that UV-cones, a single type of photoreceptor of the larval
 zebrafish eye, exhibit striking differences in their synaptic
 ultrastructure and consequent calcium to glutamate transfer function
 depending on their location in the eye. We arrive at this conclusion by
 combining serial section electron microscopy and simultaneous
 “dual-colour” 2-photon imaging of calcium and glutamate signals from the
 same synapse in vivo. We further use the functional dataset to fit a
 cascade-like model of the ribbon synapse with different vesicle pool
 sizes, transfer rates and other synaptic properties. Exploiting recent
 developments in simulation-based inference, we obtain full posterior
 estimates for the parameters and compare these across different retinal
 regions. The model enables us to extrapolate to new stimuli and to
 systematically investigate different response behaviours of various ribbon
 configurations. We also provide an interactive, easy-to-use version of
 this model as an online tool. Overall, we show that already on the
 synaptic level of single neuron types there exist highly specialized
 mechanisms which are advantageous for the encoding of different visual
 features.
DOI: 10.5061/dryad.kh1893265
title: Membrane lipid metabolism, heat shock response, and energy costs mediate the interaction between acclimatization and heat hardening response

description: Thermal plasticity on different timescales, including
 acclimation/acclimatization and heat hardening response – a rapid
 adjustment for thermal tolerance after a nonlethal thermal stress, can
 interact on organisms to improve the resilience to thermal stress.
 However, little is known about the physiological mechanisms mediating this
 interaction. To investigate underpinnings of heat hardening responses
 after acclimatization in warm season, we measured thermal tolerance
 plasticity, compared transcriptomic and metabolomic changes after heat
 hardening at 33 or 37oC followed by recovery of 3 h or 24 h in an
 intertidal bivalve Sinonovacula constricta. The clams showed explicit heat
 hardening responses after acclimatization in warm season. The higher
 inducing temperature (37oC) caused a less effective heat hardening effect
 than the inducing temperature that was closer to seasonal maximum
 temperature (33oC). Metabolomic analysis highlighted the elevated contents
 of membrane glyceropholipids in all heat hardened clams, which may help to
 maintain structure and function of membrane. Heat shock proteins (HSPs)
 tended to be up-regulated after heat hardening at 37oC but not at 33oC,
 indicating that there was no complete dependency of heat hardening effects
 on up-regulated HSPs. Enhanced energy metabolism and decreased energy
 reserves were observed after heat hardening at 37oC, suggesting more
 energy costs during exposure to higher inducing temperature which may
 restrict heat hardening effects. These results highlighted the mediating
 role of membrane lipid metabolism, heat shock responses and energy costs
 in the interaction of heat hardening response and seasonal
 acclimatization, and benefit the mechanistic understanding of evolutionary
 change and thermal plasticity during global climate change.
DOI: 10.5061/dryad.ht76hdrg5
title: Data from: Adaptations and responses of the common dandelion to low atmospheric pressure in high altitude environments

description: Atmospheric pressure is an important, yet understudied factor that may
 shape plant ecology and evolution. By growing plants under controlled
 conditions at different experimental stations in the Swiss alps, we
 evaluated the impact of ecologically realistic atmospheric pressures
 between 660 and 950 hPa on the growth and defence of different dandelion
 populations. Low atmospheric pressure was associated with reduced root
 growth and defensive sesquiterpene lactone production. Defence suppression
 only occurred in populations originating from lower altitudes. Populations
 from higher altitudes constitutively produced less sesquiterpene lactones
 and did not suffer from suppression under low atmospheric pressure.
 Synthesis. We conclude that atmospheric pressure modulates root growth and
 defence traits, and that evolutionary history shapes plant phenotypic
 responses to atmospheric pressure. Our findings have important
 implications for our understanding of altitudinal gradients and the future
 use of plants as a source of food and bioactive metabolites in
 extraterrestrial habitats.
description: Raw data: Biomass, latex quantity and latex chemical composition
 of dandelion plants growing at four experimental stations; abiotic
 conditions of the four experimental stations; description and
 environmental parameters of natural habitats of nine dandelion
 populations.
DOI: 10.5061/dryad.rjdfn2zbr
title: Supporting data for climate-driven tree mortality and fuel aridity increase wildfire's potential sensible heat flux

description: Wildfire is capable of rapidly releasing the energy stored in forests,
 with the amount of water in live and dead biomass acting as a regulator on
 the amount and rate of energy release. Here we used temperature and fuel
 moisture data to examine climate-driven changes in fuel moisture content
 over the past three decades. We then calculated the changes in energy
 release (energy release component and fire radiant energy) for two forests
 that experienced drought and bark beetle mortality and were subsequently
 burned by wildfires. We found that mortality transitioned substantial
 amounts of biomass from live to dead pools. Coupled with climate-driven
 decreases in fuel moisture content, this change in fuel availability
 increased the amount of energy that could be released during wildfire in
 these forests. Our results demonstrate that climate-driven tree mortality
 and fuel aridity may be increasing the amount of energy that is released
 during wildfire.
description: This is the code used to process publicly available data from
 GridMet, RAWS, and FIA.
DOI: 10.5061/dryad.ksn02v74j
title: Large seeds provide an intrinsic growth advantage that depends on leaf traits and root allocation

description: Seed mass and growth rate are important dimensions of plant ecological
 diversity, but their relationship remains unresolved. Negative
 relationships between relative growth rate (RGR) and seed mass are well
 established. However, RGR is size-dependent, so small-seeded species might
 achieve fast growth simply because they are initially small. Using a
 dataset of unprecedented size, sampling 382 grass species, we investigated
 seed mass and growth rate using both RGR and SGR (RGR at a specific size),
 accounting for diversity in phylogeny, ecology (e.g. life history,
 photosynthetic pathway) and environment (mean annual temperature and
 precipitation). RGR and SGR showed contrasting relationships with seed
 mass, such that large-seeded species had lower RGR but higher SGR than
 small-seeded species. However, the relationship between SGR and seed mass
 depended on leaf dry matter content (LDMC), and was only positive in
 high-LDMC species. When compared at a common size, the fast growth of
 large-seeded and low-LDMC species was associated with greater biomass
 allocation to roots in the hot, high-light environment used for our
 experiment. Photosynthetic pathway and life history contributed to
 variation in SGR, with C4 annuals having higher SGRs than C3 perennials
 regardless of seed size. Large seeds therefore afford an intrinsic growth
 advantage in species with resource-conserving leaf traits, and may provide
 a competitive edge in resource-poor environments. This work advances
 understanding of how seed mass and growth rate coevolve with other
 ecological factors.
DOI: 10.5061/dryad.t76hdr81d
title: SimPhy configuration scripts for simulations reported in the study titled: Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs

description: Many recent phylogenetic methods have focused on accurately inferring
 species trees when there is gene tree discordance due to incomplete
 lineage sorting (ILS). For almost all of these methods, and for
 phylogenetic methods in general, the data for each locus is assumed to
 consist of orthologous, single-copy sequences. Loci that are present in
 more than a single copy in any of the studied genomes are excluded from
 the data. These steps greatly reduce the number of loci available for
 analysis. The question we seek to answer in this study is: What happens if
 one runs such species tree inference methods on data where paralogy is
 present, in addition to or without ILS being present? Through simulation
 studies and analyses of two large biological data sets, we show that
 running such methods on data with paralogs can still provide accurate
 results. We use multiple different methods, some of which are based
 directly on the multispecies coalescent (MSC) model, and some of which
 have been proven to be statistically consistent under it. We also treat
 the paralogous loci in multiple ways: from explicitly denoting them as
 paralogs, to randomly selecting one copy per species. In all cases the
 inferred species trees are as accurate as equivalent analyses using
 single-copy orthologs. Our results have significant implications for the
 use of ILS-aware phylogenomic analyses, demonstrating that they do not
 have to be restricted to single-copy loci. This will greatly increase the
 amount of data that can be used for phylogenetic inference.
description: These are scripts for running SimPhy to generate gene trees given
 the species trees.