cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xd2547dj1
title: It takes time to heal a broken heart: Ventricular plasticity improves heart performance after myocardial infarction in rainbow trout, Oncorhynchus mykiss

description: Coronary arteriosclerosis is a common feature of both wild and farmed
 salmonid fishes and may be linked to stress-induced cardiac pathologies.
 Yet, the plasticity and capacity for long-term myocardial restructuring
 and recovery following a restriction in coronary blood supply is unknown.
 Here, we analyzed the consequences of acute (3 days) and chronic (from 33
 to 62 days) coronary occlusion (i.e., coronary artery ligation) on cardiac
 morphological characteristics and in vivo function in juvenile rainbow
 trout, Oncorhynchus mykiss. Acute coronary occlusion resulted in elevated
 resting heart rate and decreased inter-beat variability, which are both
 markers of autonomic dysfunction following acute myocardial ischemia,
 along with severely reduced heart rate scope (maximum – resting heart
 rate) relative to sham-operated trout. We also observed a loss of
 myocardial interstitial collagen and compact myocardium. Following
 long-term coronary- ligation, resting heart rate and heart rate scope
 normalized relative to sham-operated trout. Moreover, a distinct fibrous
 collagen layer separating the compact myocardium into two layers had
 formed. This may contribute to maintain ventricular integrity across the
 cardiac cycle, or alternatively, demark a region of the compact myocardium
 that continues to receive oxygen from the luminal venous blood. Taken
 together, we demonstrate that rainbow trout may cope with the aversive
 effects caused by coronary artery obstruction through plastic ventricular
 remodeling, which, at least in part, restores cardiac performance and
 myocardium oxygenation.
DOI: 10.5061/dryad.5tb2rbp59
title: Data on the effectiveness dispersal of synzoochorous dispersers

description: Mutualism effectiveness, the contribution of an interacting organism to
 its partner’s fitness, is defined as the number of immediate outcomes of
 the interactions (Quantity component) multiplied by the probability that
 an immediate outcome results in a new individual (Quality component).
 These components form a two-dimensional effectiveness landscape with each
 species’ location determined by its values of quantity (x-axis) and
 quality (y-axis). The current dataset includes information on the
 effectiveness of synzoochorous seed dispersal across the world. This might
 allow any user to make their own landscapes for the entire set of species
 or for specific subset of species.
description: Data collected from the literature. Dataset is a compilation of
 published studies. Effectiveness components were
 converted to common currencies. QTC is the proportion of seeds dispersed
 by a given type of disperser during a given dispersal period. QLC is the
 proportion of dispersed seeds that were cached, either by scatter hoarding
 or larder hoarding. Information on taxonomy of the two partners, Country
 where the studies were performed and some traits of both plants and
 animals is also included.
DOI: 10.7291/d13t16
title: Dataset for: A Cross-Laboratory Comparison Study of Titan Haze Analogs: Surface Energy

description: In Titan's nitrogen-methane atmosphere, photochemistry leads to the
 production of complex organic particles, forming Titan’s thick haze
 layers. Laboratory-produced aerosol analogs, or "tholins", are
 produced in a number of laboratories; however, most previous studies have
 investigated analogs produced by only one laboratory rather than a
 systematic, comparative analysis. In this study, we performed a
 comparative study of an important material property, the surface energy,
 of seven tholin samples produced in three independent laboratories under a
 broad range of experimental conditions, and explored their commonalities
 and differences. All seven tholin samples are found to have high surface
 energies, and are therefore highly cohesive. Thus, if the surface
 sediments on Titan are similar to tholins, future missions such as
 Dragonfly will likely encounter sticky sediments. We also identified a
 commonality between all the tholin samples: a high dispersive (non-polar)
 surface energy component of at least 30 mJ/m2. This common property could
 be shared by the actual haze particles on Titan as well. Given that the
 most abundant species interacting with the haze on Titan (methane, ethane,
 and nitrogen) are non-polar in nature, the dispersive surface energy
 component of the haze particles could be a determinant factor in
 condensate-haze and haze-lake liquids interactions on Titan. With this
 common trait of tholin samples, we confirmed the findings of a previous
 study by Yu et al. (2020) that haze particles are likely good cloud
 condensation nuclei (CCN) for methane and ethane clouds and would likely
 be completely wetted by the hydrocarbon lakes on Titan.
description: This dataset was collected by an Ossila goniometer and the
 contact angle data were extracted using ImageJ and the Ossila
 edge-detection software. The contact angle data were used for the surface
 energy measurement of the seven Titan haze analog samples described in the
 paper.
description: The Excel file contains 15 tabs. The first provides the final
 reduced contact angle data for the 7 samples and their calculated surface
 energies (shown in Table 3 of the paper). In the next 14 tabs, the contact
 angle data for the 7 samples for both water and diiodomethane are
 provided. These tabs can be used to recreate Figure 3 of the
 paper.<br>
DOI: 10.5061/dryad.t76hdr82c
title: Vegetation structure and fuel dynamics in fire-prone, Mediterranean-type Banksia woodlands

description: Increasing extreme wildfire occurrence globally is boosting demand to
 understand the fuel dynamics and fire risk of fire-prone areas. This is
 particularly pressing in fire-prone, Mediterranean climate-type
 vegetation, such as the Banksia woodlands surrounding metropolitan Perth,
 southwestern Australia. Despite an extensive wildland-urban interface and
 frequent fire occurrence, fuel accumulation and the spatial variation in
 fuel risk is not well quantified across the broad extent of this
 ecosystem. Using a space for time sampling approach to generate a
 chronosequence of time since fire, we selected sites that spanned across
 two distinct sandy soil types (Spearwood and Bassendean sands) and a
 rainfall gradient (550 to 750 mm north–south). We examined 82
 sites in Banksia woodlands, southwestern Australia. Of the 82 sites, 44
 burnt during the measurement period (2016 to 2021), which provided the
 opportunity for fuel measurements following fire (resulting in total
 N = 126). We wanted to answer two key questions: 1) How
 do measures of fuel load (mass) and arrangement (structure and continuity)
 vary across space and time, particularly with respect to time since the
 last fire? 2) How do biophysical drivers, such as soil type and rainfall,
 influence fuel accumulation and arrangement, and do these covariates
 improve litter fuel modelling beyond traditional asymptotic models? We
 found that fine surface fuel loads (litter and small twigs) differed
 between sand types, accumulating faster and reaching a higher peak on
 Spearwood sands (7–9 Mg ha−1) compared to Bassendean
 sands (6–7 Mg ha−1). Shrub layer fuel loads also
 accumulated faster on Spearwood sands than on Bassendean sands. While
 shrub layer fuels on Spearwood sands peaked at 14 years and
 declined thereafter, those on Bassendean sand did not decline over time
 but have lower overall connectivity. Total fine fuels (fine surface plus
 fine shrub layer fuels) had no significant decline over the same time
 period, on either sand type. Total fine fuel loads reached a peak of
 9–10 Mg ha−1 between 13- and 20-years following
 fire, depending on the underlying sand type. Our quantitative fuel
 accumulation models confirmed the strength of time since fire as a
 predictor of hazard, but nonetheless included up to 40% unexplained
 variance. Importantly, while components fluctuated over time, the combined
 total of fine fuels did not decline with the long absence of fire,
 suggesting fire risk does not necessarily decrease in long unburned
 vegetation.
DOI: 10.5061/dryad.v41ns1rxp
title: Leaf water potential Cerrado and Semi-decidious forest

description: Individual leaf water potentials and VPD for species along a
 forest-savanna gradient.
DOI: 10.5061/dryad.mkkwh711w
title: Viral RefSeq databases for Centrifuge, Kraken2 and DIAMOND

description: Owing to technological advances in ancient DNA, it is now possible to
 sequence viruses from the past to track down their origin and evolution.
 However, ancient DNA data is considerably more degraded and contaminated
 than modern data making the identification of ancient viral genomes
 particularly challenging. Several methods to characterise the modern
 microbiome (and, within this, the virome) have been developed; in
 particular, tools that assign sequenced reads to specific taxa in order to
 characterise the organisms present in a sample of interest. While these
 existing tools are routinely used in modern data, their performance when
 applied to ancient microbiome data to screen for ancient viruses remains
 unknown.  In this work, we conducted an extensive simulation
 study using public viral sequences to establish which tool is the most
 suitable to screen ancient samples for human DNA viruses. We compared the
 performance of four widely used classifiers, namely Centrifuge, Kraken2,
 DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the
 corresponding viruses. To do so, we simulated reads by adding noise
 typical of ancient DNA to a set of publicly available human DNA viral
 sequences and to the human genome. We fragmented the DNA into different
 lengths, added sequencing error and C to T and G to A deamination
 substitutions at the read termini. Then we measured the resulting
 sensitivity and precision for all classifiers.  Across most
 simulations, more than 228 out of the 233 simulated viruses are recovered
 by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which
 recovers only around one third. Overall, Centrifuge and Kraken2 have the
 best performance with the highest values of sensitivity and precision. We
 found that deamination damage has little impact on the performance of the
 classifiers, less than the sequencing error and the length of the reads.
 Since Centrifuge can handle short reads (in contrast to DIAMOND and
 Kraken2 with default settings) and since it achieves the highest
 sensitivity and precision at the species level across all the simulations
 performed, it is our recommended tool. Regardless of the tool used, our
 simulations indicate that, for ancient human studies, users should use
 strict filters to remove all reads of potential human origin. Finally, we
 recommend to verify which species are present in the database used, as it
 might happen that default databases lack sequences for viruses of
 interest.
DOI: 10.5061/dryad.8kprr4xpz
title: Dispersal and life history of brown widow spiders in dated invasive populations on two continents

description: Theory and empirical work suggest that behaviours such as dispersal and
 exploration are predictors of invasive success, and that behaviours may
 shift predictably after invasive populations have established and spread.
 However, there are limited data on temporal patterns in the distribution
 of behavioural traits linked to the timeline of establishment of invasive
 species. We examine dispersal and exploration, along with life history
 traits that may be linked to behaviour, across multiple invasive
 populations of the brown widow spider (Latrodectus geometricus). This
 global invader has established populations across the United States and
 Israel. Using this temporal and spatial variation, we tested predictions
 about changes in suites of traits over establishment time. We compared
 trait distributions of four U.S. populations of L. geometricus to patterns
 in four populations in Israel. We predicted that selective filters during
 the invasion process would result in more dispersive, more exploratory
 spiders that are larger and more fecund in recently established
 populations, but, if tradeoffs occur, dispersal would be favoured at the
 expense of fecundity and size in recent populations. We found more
 frequent and faster dispersal in more recently established populations in
 Israel, but not the United States. Spiders in more recently established
 populations in Israel were larger than those in older populations, but
 there were no consistent patterns across U.S. populations. However, there
 was evidence in both the U.S. and Israel for differing tradeoffs among
 fecundity, dispersal, and size. In more recently-established populations,
 spiders had lower fecundity than expected based on body size, but were
 more variable in resource allocation to egg sacs. The results suggest that
 in some populations, trade-offs underlying dispersal, fecundity, and body
 size are shaped by the time interval, and thus the number of generations,
 since establishment, with implications for the role of evolutionary
 processes in invasion success.
description: These data are of behaviour, life history, and size of eight
 invasive <i>Latrodectus geometricus </i>(brown widow spider)
 populations. We collected these data through laboratory observations of
 dispersal propensity and time to disperse, time to build a web in a new
 environment, fecundity (number of eggs in an egg sac), patella-tibia
 length of adult females, and spiderling cephalothorax width. The data are
 raw values from lab observations and measurements.
description: The readme file contains an explanation of each of the variables
 in the dataset and its measurement units. Missing or unavailable values
 are indicated with "null". Information on how the measurements
 were done can be found in the associated manuscript referenced
 above.
DOI: 10.5061/dryad.j3tx95xfw
title: Immigrant males’ memory acts to reduce ranging overlap and mating competition in wild baboons

description: Mechanistic models suggest that information acquired by animals
 (“knowledge”) could shape home range patterns and dynamics, and how
 neighbours share space. In social species this would suggest that
 immigrants could bring new knowledge into social groups, potentially
 affecting the dynamics of home range overlap. We tested this “immigrant
 knowledge hypothesis” in a wild population of chacma baboons (Papio
 ursinus). We used data collected between 2005 and 2013 on two neighbouring
 troops in Namibia, comprising GPS records of daily ranges, male natal
 origins, daily females’ reproductive status, and a satellite index of
 vegetation growth. We found that when the ratio of fertile females to
 adult males in the focal troop increased (i.e. increasing inter-troop
 mating competition costs for focal troop males), the focal troop tended to
 overlap less with a neighbouring troop’s home range only when the alpha
 male had immigrated from that neighbouring troop and so was
 “knowledgeable” about its home range. When the alpha male was “not
 knowledgeable” the reverse was observed, with troops showing greater
 overlap, most likely reflecting an influence of fertile females on ranging
 patterns. Our findings support the immigrant knowledge hypothesis of group
 ranging behaviour, and suggest that dispersal and spatial memory may
 sometimes act to increase rather than decrease spatial segregation between
 groups. Very few previous studies have reported an effect of mating
 competition on ranging dynamics in social species, perhaps because
 previous studies did not consider divergent adaptive interest among group
 members and how they can be solved through collective-decision processes.
DOI: 10.5061/dryad.7sqv9s4t9
title: Data from: Intraspecific trait changes have large impacts on community functional composition but do not affect ecosystem function

description: 1.    Plant functional traits can provide a
 mechanistic understanding of community responses to global change and of
 community effects on ecosystem functions. Nitrogen enrichment typically
 shifts trait composition by promoting the dominance of acquisitive plants
 (high specific leaf area [SLA] and low leaf dry matter content [LDMC]),
 translating into high biomass production. Changes in mean trait values can
 be due to shifts in species identity, relative abundances and/or
 intraspecific trait values. However, we do not know the relative
 importance of these shifts in determining trait responses to environmental
 changes, or trait effects on ecosystem functioning, such as biomass
 production.  2.    We quantified the
 relative importance of species composition, abundance and intraspecific
 shifts in driving variation in SLA and LDMC, and how these shifts affected
 above- and belowground biomass. We measured traits in a grassland
 experiment manipulating nitrogen fertilisation, plant species richness,
 foliar fungal pathogen removal and sown functional composition (slow vs.
 fast species). We fitted structural equation models to test the importance
 of abundance and intraspecific shifts in determining 1) responses of
 functional composition to treatments and 2) effects on above and
 belowground biomass.   3.    We found
 that species intraspecific shifts were as important as abundance shifts in
 determining change in functional composition (community weighted mean
 trait values), and even had large effects compared to substantial initial
 variation in sown trait composition. Intraspecific trait shifts resulted
 in convergence towards intermediate SLA in diverse communities; although
 convergence was reduced by nitrogen addition and enhanced by pathogen
 removal. In contrast, large intraspecific shifts in LDMC were not
 influenced by the treatments. However, despite large responses,
 intraspecific trait shifts had no effect on above or belowground biomass.
 Only interspecific trait variation affected functioning: belowground
 biomass was reduced by SLA and increased by LDMC, while aboveground
 biomass was increased by SLA.  4.  
  Our results add to a growing body of literature showing large
 species intraspecific trait variation and emphasise the importance of
 using field sampled data to determine community functional composition.
 However, they also show that intraspecific variation does not necessarily
 affect ecosystem functioning and therefore response-effect trait
 relationships may differ between vs. within species.
description: Some details on calculations are in the ReadMe file. However, for
 full details on data collection see the asoociated publication.
description: Please see the ReadMe file for a description of the three
 datasets included and meta data on the variables.
DOI: 10.5061/dryad.k98sf7m70
title: Data from: Are genetic variation and demographic performance linked?

description: Quantifying the empirical relationships between genetic variation and
 population viability is important from both basic biological and applied
 conservation perspectives, yet few populations have been monitored with
 both long-term demographic and population genetics approaches. Here, we
 present eight years of historical demographic data from five populations
 of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial
 plant endemic to Montana, USA, and use integral projection models to
 estimate the stochastic population growth rate (λS) and extinction risk of
 each population. We combine these demographic estimates with previously
 published metrics of genetic variation in the same populations to test
 whether genetic diversity within populations is linked to demographic
 performance. Our results show that in this predominantly inbred species,
 genetics and demography are not strongly correlated, suggesting that more
 inbred populations are not necessarily less viable or at higher extinction
 risk than more genetically diverse populations. Interestingly, however, a
 contemporary re-census revealed that, among these populations, genetic
 rather than demographic parameters were better predictors of current
 population density, with populations harboring greater genetic diversity
 maintaining denser populations at present. In the absence of evidence for
 inbreeding depression decreasing population viability in this species, we
 recommend conservation of distinct, potentially locally adapted
 populations of B. fecunda rather than alternatives such as translocations
 or reintroductions.
description: Raw demographic
 data were collected by labeling wild <em>Boechera fecunda
 </em>plants and tracking them from 1990–1997 to monitor survival,
 growth, reproduction, and recruitment in five natural populations. Derived
 demographic summary statistics for each population were estimated using
 integral projection models with parametric bootstrapping. All code to
 process data and calculate derived variables is included in this
 archive. Complementary genetic summary statistics for
 the five focal populations were extracted from a previous publication
 (Song & Mitchell-Olds 2007, "High genetic diversity and
 population differentiation in <em>Boechera fecunda</em>, a
 rare relative of <em>Arabidopsis</em>",
 <em>Molecular Ecology</em>).
description: Usage notes are provided in the enclosed README.txt file.
DOI: 10.5061/dryad.j0zpc86g2
title: Parallel processing by distinct classes of principal neurons in the olfactory cortex

description: Understanding how distinct neuron types in a neural circuit process and
 propagate information is essential for understanding what the circuit does
 and how it does it. The olfactory (piriform, PCx) cortex contains two main
 types of principal neurons, semilunar (SL) and pyramidal (PYR) cells. SLs
 and PYRs have distinct morphologies, local connectivity, biophysical
 properties, and downstream projection targets. Odor processing in PCx is
 thought to occur in two sequential stages. First, SLs receive and
 integrate olfactory bulb input and then PYRs receive, transform, and
 transmit SL input. To test this model, we recorded from populations of
 optogenetically identified SLs and PYRs in awake, head-fixed mice.
 Notably, silencing SLs did not alter PYR odor responses, and SLs and PYRs
 exhibited differences in odor tuning properties and response
 discriminability that were consistent with their distinct embeddings
 within a sensory-associative cortex. Our results therefore suggest that
 SLs and PYRs form parallel channels for differentially processing odor
 information in and through PCx.
description: The dataset contains extracellular recordings of layer II
 piriform cortex neurons in awake, head-fixed Ntng1-Cre mice. Recordings
 were made using 32-channel Neuronexus probes and sorted using
 Spyking-Circus. Semilunar cells were opto-tagged during recordings and the
 sorted units have been categorized as either semilunar or superficial
 pyramidal based on their responses to light.
description: Description of data organization and notes for usage are provided
 in NagappanFranks_eLife2021_dataDocumentation.pdf