cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vdncjsxs4
title: Processes at the soil-root interface determine the different responses of nutrient limitation and metal toxicity in forbs and grasses to nitrogen enrichment

description: Nutrient limitation and metal toxicity have been implicated in changes of
 grassland communities by nitrogen (N) deposition. Belowground processes,
 especially those at the soil-root interface, play important roles in
 determining variation in nutrient concentrations in plants. However, few
 studies have specifically focused on the roles of these processes in
 mineral-element acquisition in grassland plants in response to N
 enrichment. Here we investigated the contributions of belowground
 processes at the soil-root interface to the differential acquisition of
 phosphorus (P), calcium (Ca) and manganese (Mn) by forbs and grasses of a
 temperate steppe in response to N addition by combining field and
 glasshouse experiments. Nitrogen addition increased the concentrations of
 both leaf P ([P]) and Mn ([Mn]) and decreased leaf [Ca] of forbs, while it
 had little effects on leaf concentrations of these elements in grasses.
 Nitrogen addition led to a higher activity of acid phosphatase in the
 rhizosphere of forb, and greater release of protons and carboxylates from
 forb roots than grass roots, contributing to the differential [P], [Ca]
 and [Mn] in leaves of forbs and grasses. Applying oxalate to soil to
 simulate the release of carboxylates by N enrichment enhanced [P] and
 [Mn], and decreased [Ca] in the soil solution. However, addition of
 hydrogen-ion increased [P], [Mn] and [Ca] in the soil solution. Lime
 addition mitigated the N addition-induced soil acidification, while it did
 not abolish the stimulatory effect of short-term N addition on leaf [P]
 and [Mn] of forbs. Therefore, we conclude that differences in the
 ecophysiological processes at the soil-root interface account for changes
 in leaf [P], [Ca] and [Mn] under short-term N addition, and that soil
 acidification aggravates the responses of these elements, especially [Ca]
 and [Mn], to long-term N enrichment. Synthesis: Our results highlight the
 contribution of belowground processes, especially those at the soil-root
 interface, to variation in plant element concentrations between dominant
 forbs and grasses in the temperate steppe. These findings greatly enhance
 our mechanistic understanding of the effects of N deposition on grassland
 communities.
description: The dataset was collected from long-term nitrogen addition
 experiments in a temperate steppe, and we included the original data used
 for publication.
DOI: 10.5061/dryad.8gtht76mt
title: Anti-predator behaviour depends on male weapon size

description: Tonic immobility and escape are adaptive anti-predator tactics used by
 many animals. Escape requires movement, whereas tonic immobility does not.
 If anti-predator tactics relate to weapon size, males with larger weapons
 may adopt tonic immobility, whereas males with smaller weapons may adopt
 escape. However, no study has investigated the relationship between weapon
 size and anti-predator tactics. In this study, we investigated the
 relationship between male weapon size and tonic immobility in the beetle
 Gnathocerus cornutus. The results showed that tonic immobility was more
 frequent in males with larger weapons. Although most studies of tonic
 immobility in beetles have focused on the duration, rather than the
 frequency, tonic immobility duration was not affected by weapon size in G.
 cornutus. Therefore, this study is the first to suggest that the male
 weapon trait affects anti-predator tactics.
DOI: 10.5061/dryad.6wwpzgmwr
title: Community composition of arctic root-associated fungi mirrors host plant phylogeny

description: The number of plant species regarded as non-mycorrhizal increases at
 higher latitudes, and several plant species in the High-Arctic Archipelago
 Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and
 18S gene markers to survey which fungi, as well as other micro-eukaryotes,
 were associated with roots of 31 arctic plant species not usually regarded
 as mycorrhizal in Svalbard. We assessed to what degree the root-associated
 fungi showed any host preference and whether the phylogeny of the plant
 hosts may mirror the composition of root-associated fungi. Fungal
 communities were largely structured according to host plant identity and
 to a less extent by environmental factors. We observed a positive
 relationship between the phylogenetic distance of host plants and the
 distance of fungal community composition between samples, indicating that
 the evolutionary history of the host plants plays a major role for which
 fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S
 rRNA gene marker showed that chytrid fungi were prevalently associated
 with plant roots, together with a wide spectrum of amoeba-like protists
 and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi
 are present also in arctic environments in low abundance.
description: ITS2 fungal amplicon data, and general eukarytic 18S V4 data from
 the roots of 31 arctic plant species.
DOI: 10.5061/dryad.8cz8w9gnh
title: Pathogen dynamics across the diversity of ageing

description: Reproduction, mortality and immune function often change with age, but do
 not invariably deteriorate. Across the tree of life, there is extensive
 variation in age-specific performance and changes to key life-history
 traits. These changes occur on a spectrum from classic senescence, where
 performance declines with age, to juvenescence, where performance improves
 with age. Reproduction, mortality and immune function are also important
 factors influencing the spread of infectious disease, yet there exists no
 comprehensive investigation into how the ageing spectrum of these traits
 impacts epidemics.We used a model laboratory infection system to compile
 an ageing profile of a single organism, including traits directly linked
 to pathogen resistance, and those that should indirectly alter pathogen
 transmission by influencing demography. We then developed generalizable
 epidemiological models demonstrating that different patterns of ageing
 produce dramatically different transmission landscapes: in many cases
 ageing can reduce the probability of epidemics, but it can also promote
 severity. This work provides context and tools for use across taxa by
 empiricists, demographers and epidemiologists, advancing our ability to
 accurately predict factors contributing to epidemics, or the potential
 repercussions of senescence manipulation.
description: Data were collected and then entered into excel. They were double
 checked prior to commencing analysis. JC collected, entered and double
 checked data. Statistical analysis was conducted in
 R. Simulation model development and derivations were
 carried out in Mathematica and R.
description: controls_infected.csv is the file for the analysis of the force
 of mortality in infected and uninfected individuals. 
 mat.sen.old.mums.csv is the file for the analysis of reproduction
 in the maternal generation.  mat.effect.sen.data.csv is
 the file for the analysis of offspring performance. 
 pathogen.dynamics.ageing.R is the script for all experimental
 analysis, statistical model selection, visualisation and data manipulation
 of the above csv files. Packages necessary to carry this out are listed at
 the top of the file.  Next.Gen.Matrix.Method.nb is the
 Mathematica Notebook which includes the formulation and analysis of the
 NGM.
DOI: 10.5061/dryad.bzkh1896t
title: Automated improvement of stickleback reference genome assemblies with Lep-Anchor software

description: We describe an integrative approach to improve contiguity and haploidy of
 a reference genome assembly and demonstrate its impact with practical
 examples. With two novel features of Lep-Anchor software and a
 combination of dense linkage maps, overlap detection and bridging
 long reads we generated an improved assembly of the nine-spined
 stickleback (Pungitius pungitius) reference genome. We were
 able to remove a significant number of haplotypic contigs, detect
 more genetic variation and improve the contiguity of the genome,
 especially that of X chromosome. However, improved scaffolding
 cannot correct for mosaicism of erroneously assembled contigs,
 demonstrated by a de novo assembly of a 1.7 Mbp inversion.
 Qualitatively similar gains were obtained with the genome of
 three-spined stickleback (Gasterosteus aculeatus). The utility of
 genome-wide sequencing data in biological research depends heavily on
 the quality of the reference genome. Although the reference
 genomes have improved, it is evident that the assemblies could still be
 refined, especially in non-model study organisms. 
description: This submission contains a snapshot of computer code
 and instructions for automated improvement of reference genome assemblies
 and scripts for reproducing the published analyses.  An up-to-date version
 is available at https://github.com/mikkokivikoski/NSP_V7.
DOI: 10.5061/dryad.8sf7m0ckf
title: Perceived and actual fighting ability: determinants of success via decision, knockout or submission in human combat sports

description: Animal contest theory assumes individuals to possess accurate information
 about their own fighting ability or resource holding potential (RHP) and,
 under some models, that of their opponent. However, due to the difficulty
 of disentangling perceived and actual RHP in animals, how accurately
 individuals are able to assess RHP remains relatively unknown.
 Furthermore, it is not just individuals within a fight that evaluate RHP.
 Third party observers evaluate the fight performance of conspecifics in
 order to make behavioural decisions. In human combat sports, when fights
 remain unresolved at the end of the allotted time, bystanders take a more
 active role, with judges assigning victory based on their assessment of
 each fighter's performance. Here, we use fight data from mixed
 martial arts in order to investigate whether perceived fighting
 performance (judges’ decisions) and actual fighting success (fights ending
 in knock out or submission) are based on the same performance traits,
 specifically striking skill and vigour. Our results indicate that both
 performance traits are important for victory, but that vigour is more
 important for fights that resolve naturally. These results suggest that
 while similar traits are important for fighting success across the board,
 vigour is undervalued in judges’ perceptions of RHP.
description: Data was collated from UFC.com.
DOI: 10.15468/dl.q7e5xa
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Calamus simplicifolius"
 ]
}

 The dataset includes 28 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002579-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bzkh1896v
title: The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

description: Aside from polyploidy, transposable elements are the major drivers of
 genome size increases in plants. Thus, understanding the diversity and
 evolutionary dynamics of transposable elements in sunflower (Helianthus
 annuus L.), especially given its large genome size (∼3.5 Gb) and
 the well‐documented cases of amplification of certain transposons within
 the genus, is of considerable importance for understanding the
 evolutionary history of this emerging model species. By analyzing
 approximately 25% of the sunflower genome from random sequence reads and
 assembled bacterial artificial chromosome (BAC) clones, we show that it is
 composed of over 81% transposable elements, 77% of which are long terminal
 repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction
 in BAC clones harboring genes is disproportionately composed of
 chromodomain‐containing Gypsy LTR retrotransposons
 (‘chromoviruses’), and the majority of the intact chromoviruses contain
 tandem chromodomain duplications. We show that there is a bias in the
 efficacy of homologous recombination in removing LTR retrotransposon DNA,
 thereby providing insight into the mechanisms associated with transposable
 element (TE) composition in the sunflower genome. We also show that the
 vast majority of observed LTR retrotransposon insertions have likely
 occurred since the origin of this species, providing further evidence that
 biased LTR retrotransposon activity has played a major role in shaping the
 chromatin and DNA landscape of the sunflower genome. Although our findings
 on LTR retrotransposon age and structure could be influenced by the
 selection of the BAC clones analyzed, a global analysis of random sequence
 reads indicates that the evolutionary patterns described herein apply to
 the sunflower genome as a whole.
DOI: 10.5061/dryad.6hdr7sqz8
title: The macroecology of fish migration

description: Aim: We still lack a consensus on the main variables driving changes in
 migratory strategies. Different hypotheses have been proposed:
 productivity, energy, environmental heterogeneity, and genetic
 predisposition. This work takes an integrative view and analyzes
 migrations from a macroecological perspective estimating the extent to
 which different environmental variables and historic factors influence
 migratory life histories. Location: Global Time period: Current Major taxa
 studied: Actinopterygian fishes Methods: Using public domain museum
 records, global repositories, and global measures of temperature,
 productivity, precipitation and heterogeneity, we spatially analyzed the
 distribution of anadromous, catadromous, amphidromous, potamodromous and
 oceanodromous migratory fish using 1676 species and compared it to 1616
 non-migratory fishes. After analyzing the individual roles of productivity
 and temperature in shaping biodiversity, we conducted path analyses
 including several environmental variables and principal coordinates of
 phylogenetic structure (PCPS). Results: The different migratory strategies
 are not evenly distributed around the globe and phylogeny is a relevant
 variable in shaping current patterns. Productivity is positively related
 to species richness, except for anadromy and potamodromy, where we
 observed a unimodal curve. Temperature significantly drives migratory
 species richness (except for anadromy). The role of environmental
 heterogeneity, measured as temperature seasonality and annual range is
 strongest for anadromous species, which helps explain their skewed
 distribution towards higher latitudes and why the kinetic-energy
 hypothesis fails in explaining their richness patterns. Main conclusions:
 Overall, migratory fish richness can be explained by the interaction of
 multiple variables, such as productivity, temperature, environmental
 heterogeneity, and the role of phylogeny, but these variables interact
 differentially in each strategy, diverging mostly for the anomalous
 anadromous fishes. Integrating these results into a global framework to
 better understand the evolutionary and ecological dynamics of migration
 will help with predicting responses to anthropogenic climate change
description: See readme.txt file.
description: Tutorials introducing methods to visualize and analyze the data
 provided are available
 at https://sites.google.com/view/dominique-alo/DominiqueAloBlog.
DOI: 10.5061/dryad.612jm641x
title: Canopy structure and forest understory conditions in a wet Amazonian forest – no change over the last 20 years

description: Climate change is altering forest dynamics in the tropics, with large
 potential impacts on forest structure and understory conditions. However,
 we found that canopy height distribution and openness remained stable over
 two decades in the western Amazon, and that gap creation rates would need
 to increase 300% before affecting equilibrium.
description: Data were collected in the western part of the Amazon basin in
 Yasuní National Park in Ecuador (0°40’29” S, 76°23’51”
 W). Canopy height, canopy openness and understory density data were recorded in six 10 x 250m plots (1.5 ha in total) in 1998 and again in 2019 (labeled census 1 and 2 in the dataset, respectively). One of the plots was located in a seasonally inundated floodplain forest, and the five others covered ridge tops, slopes and bottomland areas. Each plot was divided into a 5 x 5m grid. For each grid square we measured maximum canopy height and average height to the centre of the tree crowns using a clinometer and measuring tape. Heights were assigned to the following classes: 0–5m, 5–10m, 10–20m and &gt;20m. In the centre of each square we recorded canopy openness 1 m above the ground using crown illumination ellipses (CIE; see main text), where values &gt;1.0 indicated areas with visible gaps in the canopy and elevated light conditions. Understory vegetation density was classified as either dense, herbaceous, liana-tangle, or sparse. Here ‘herbaceous’ was used for areas covered with herbs (e.g. Marantaceae spp.), but with very few woody plants, and ‘liana-tangle’ was used for areas where the ground was densely covered with lianas, but with only a few tree saplings. We constructed two different transition matrices <b><i>A</i></b> to study the projected effects of changes in canopy dynamics, one for maximum and one for average canopy height. The matrices were based on observed probabilities of transitions between height classes for all 600 grid squares between 1998 and 2019. To assess how increased creation of gaps would influence the asymptotic height class distribution, we used matrix modelling to conduct a perturbation experiment by gradually altering the number of squares with average height 10–20m that were converted to gaps with 0–5m tall canopy over a 20-y period.
description: There are no missing values in the data, but additional data are
 available for some of the plots (measurements of canopy height outside the
 plot squares used in this study, and for additional censuses). These can
 be provided upon request. The baselines of the plots
 are marked with grey plastic tubes in the field.
DOI: 10.5061/dryad.wwpzgmshb
title: Immune challenges increase network centrality in a queenless ant

description: Social animals display a wide range of behavioural defences against
 infectious diseases, some of which inherently increase social contacts
 with infectious individuals (e.g., mutual grooming), while others decrease
 them (e.g., social exclusion). These defences often rely on the detection
 of infectious individuals, but this can be achieved in several ways that
 are difficult to differentiate. Here, we combine non-pathogenic immune
 challenges with automated tracking in colonies of the clonal raider ant to
 ask whether ants can detect the immune status of their social partners and
 to quantify their behavioural responses to this perceived infection risk.
 We first show that a key behavioural response elicited by live pathogens
 (allogrooming) can be qualitatively recapitulated by immune challenges
 alone. Automated scoring of interactions between all colony members
 reveals that this behavioural response increases the network centrality of
 immune-challenged individuals through a general increase in physical
 contacts. These results show that ants can detect the immune status of
 their nestmates and respond with a general “caring” strategy, rather than
 avoidance, towards social partners that are perceived to be infectious.
 Finally, we find no evidence that changes in cuticular hydrocarbon
 profiles drive these behavioural effects.
description: Survival of individuals was scored manually. Grooming received by
 focal ants was manually scored from video recordings using BORIS software
 5.1.0. Other behavioural metrics were calculated from automatedly tracked
 trajectories of all ants recorded with the tracking software anTraX. Mass
 spectra of cuticular hydrocarbons were acquired and analysed with the
 software ChemStation G1701AA v. A.03.00.
DOI: 10.5061/dryad.7pvmcvdrb
title: Dynamic encoding of social threat and spatial context in the hypothalamus - calcium activity recordings and behavioural dataset

description: Social aggression and avoidance are defensive behaviors expressed by
 territorial animals in a manner appropriate to spatial context and
 experience. The ventromedial hypothalamus controls both social aggression
 and avoidance, suggesting that it may encode an general internal state of
 threat modulated by space and experience. Here we show that neurons in the
 mouse ventromedial hypothalamus are activated both by the presence of a
 social threat as well as by a chamber where social defeat previously
 occurred. Moreover, under conditions where the animal could move freely
 between a home and defeat chamber, firing activity emerged that predicted
 the animal’s position, demonstrating the dynamic encoding of spatial
 context in the hypothalamus. Finally, we found that social defeat induced
 a functional reorganization of neural activity as optogenetic activation
 could elicit avoidance after, but not before social defeat. These findings
 reveal how the hypothalamus dynamically encodes spatial and sensory cues
 to drive social behaviors.
description: Please check ReadMe file uploaded with the dataset and methods
 section in the paper "Dynamic encoding of social threat and spatial
 context in the hypothalamus"
description: Please check ReadMe file attached with dataset and methods
 section in "Dynamic encoding of social threat and spatial context in
 the hypothalamus"