cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm63xsj6n
title: First field-based evidence that the seagrass-lucinid mutualism can mitigate sulfide stress in seagrasses

description: Seagrass meadows form vital ecological components of coastal zones
 worldwide, but are rapidly declining. Large-scale seagrass diebacks have
 been related to accumulation of toxic sulfide in the sediment, a
 phenomenon predicted to occur more frequently in the near future due to
 ongoing global warming and increasing organic loading of coastal systems
 worldwide. Recently, a facultative mutualism between seagrasses and
 lucinid bivalves with endosymbiotic sulfide-consuming gill bacteria was
 discovered that may prevent toxic sulfide accumulation in seagrass
 sediments. Yet, direct field-based evidence for the importance of this
 mutualism in alleviating sulfide stress in seagrasses is currently
 lacking, as well as how its role may change when sediment sulfide levels
 increase due to environmental change. Here, we investigated the sulfide
 detoxification function of this seagrass-lucinid mutualism and its
 resilience to organic-loading induced sulfide stress in a temperate lagoon
 system (Thau lagoon, France), using a correlative field survey and a full
 factorial field experiment. The field survey revealed a strong positive
 correlation between seagrass above-ground biomass and lucinid densities,
 and pore water sulfide concentrations close to zero at all sites.
 Furthermore, the field experiment revealed that addition of organic matter
 (starch mixed with sucrose) increased sedimentary sulfide intrusion into
 seagrass (Zostera noltei) leaves (a proxy for sulfide stress), while
 experimentally enhanced lucinid densities reduced sulfide intrusion,
 regardless of addition of organic matter. Moreover, addition of organic
 matter reduced seagrass rhizome biomass and increased pore water sulfide
 levels, lucinid tissue sulfur content, lucinid condition (expressed as
 flesh/shell dry weight ratio), and total lucinid biomass, while
 enhancement of lucinid densities reduced lucinid condition. These results
 provide the first field-based evidence that lucinid bivalves and their
 sulfide-oxidizing gill symbionts mitigate sulfide stress in seagrasses,
 and suggests that the dependence of seagrass on this seagrass-lucinid
 mutualism will increase under conditions of enhanced sediment sulfide
 production, as predicted for the near future. Therefore, we suggest that
 awareness of the ecological importance of the seagrass-lucinid mutualism
 may be instrumental for designing new measures for improving long-term
 restoration success and seagrass resilience to global change.
description: The ReadMe file describes the data files accompanying the above
 publication.
DOI: 10.5061/dryad.34tmpg4gc
title: Evolution of ammonia-oxidizing archaea related to global events

description: Ammonia-oxidizing archaea (AOA) are chemolithoautotrophs that dominate
 nitrification in today’s low ammonium ocean, playing critical roles in the
 global nitrogen cycle, alongside ammonia-oxidizing bacteria (AOB) that
 favor higher ammonium environments. Nitrification may have occurred soon
 after the origin of oxygenic photosynthesis and provided fundamental
 nutrients for the emergence of eukaryotic organisms in the Proterozoic;
 however, the timing of biological evidence remains unclear. Here we show
 using phylogenetic models that AOA occurred ~1,165 (1,928-880) Mya in a
 terrestrial geothermal environment, ~652 (767-554) Mya in low temperature
 soil niches, and ~509 (629-412) Mya in aquatic environments. AOA
 originated in marine settings around 362 (478-274) Mya, which was followed
 by the rapid diversification of shallow- and deep- subgroups around 315
 (478-207) Mya and 309 (460-207) Mya, respectively, leading to today’s
 domination of AOA in global oceans. The radiation of thermophilic AOA into
 mesophilic terrestrial soil may have been triggered by the 'snowball
 Earth' events of the Cryogenian Period and their 'hothouse
 Earth' aftermaths. The radiation of AOA into the deep ocean had to
 await the persistent oxygenation of the deep ocean that was associated
 with the rise of land plants. Our genetic analyses integrated with a
 geochemical data and a modeling framework offers an intriguing linkage
 between microbial evolution and the belated oxygenation of the deep ocean
 in the Paleozoic Era.
DOI: 10.5061/dryad.z612jm68b
title: Data from: Burning savanna for avian species richness and functional diversity

description: Prescribed fire is used throughout fire-prone landscapes to conserve
 biodiversity. Current best practice in managing savanna systems advocates
 methods based on the assumption that increased fire-mediated landscape
 heterogeneity (pyrodiversity) will promote biodiversity. However,
 considerable knowledge gaps remain in our understanding of how savanna
 wildlife responds to the composition and configuration of pyrodiverse
 landscapes. The effects of pyrodiversity on functional diversity has
 rarely been quantified and assessing this relationship at a landscape
 scale which is commensurate with fire management is important for
 understanding mechanisms underlying ecosystem resilience. Here, we assess
 the impact of spatiotemporal variation in a long-term fire regime on avian
 diversity in North West Province, South Africa. We examined the
 relationship between (a) species richness, (b) three indices of functional
 diversity (i.e., functional richness, functional evenness and functional
 dispersion) and four measures of pyrodiversity, the spatial extents of
 fire age-classes, and habitat type at the landscape-scale. We then used
 null models to assess differences between observed and expected functional
 diversity. We found that the proportion of newly-burned (&lt;1-year
 post-fire), old, unburned (≥10 years post-fire), and woodland habitat on
 the landscape predicted species and functional richness. Species richness
 also increased with the degree of edge contrast between patches of varying
 fire age, while functional dispersion increased with the degree of patch
 shape complexity. Lower than expected levels of functional richness
 suggest that habitat filtering is occurring, resulting in functional
 redundancy across our study sites. We demonstrate that evaluating
 functional diversity and redundancy is an important component of
 conservation planning as they may contribute to previously reported fire
 resilience. Our findings suggest that it is the type and configuration,
 rather than the diversity, of fire patches on the landscape that promote
 avian diversity and conserve ecological functions. A management approach
 is needed that includes significant coverage of adjacent newly-burned and
 older, unburned savanna habitat; the latter, in particular, is
 inadequately represented under current burning practices.
description: Data was collected using point counts. Functional diversity
 metrics were estimated using the R package 'FD'.
description: Please see ReadMe file for a description of the data.
DOI: 10.5061/dryad.8cz8w9gkv
title: Predator defense is shaped by risk, brood value and social group benefits in a cooperative breeder

description: Predation is a major cause of mortality and nest failure in birds.
 Cooperative predator defense can enhance nest success and adult survival,
 but since it is inherently risky, dynamic risk assessment theory predicts
 that individuals modify defense behavior according to risk posed by the
 predator. Parental investment theory on the other hand predicts that
 reproductive payoffs (brood value) determine investment in nest defense.
 We propose that in cooperative breeders, fitness benefits deriving from
 survival of other group members may additionally influence defense
 behavior (social group benefits theory). We tested predictions of these
 theories in the cooperatively breeding purple-crowned fairy-wren, Malurus
 coronatus, where brood value is higher for breeders, but social group
 benefits more important for helpers. We recorded experimentally-induced
 individual defense behaviors in response to predator models presented near
 nests, representing differing levels of threat to nests and adults. As
 predicted, (i) individuals engaged in less risky defenses when
 encountering a more dangerous predator (dynamic risk assessment theory);
 (ii) individuals defended older broods more often, and breeders defended
 more than helpers (parental investment theory); and (iii) helpers were
 more likely to respond to a predator of adults (social group benefits
 theory). Our findings highlight that predator defense in cooperative
 breeders is complex, shaped by the combination of immediate risk and
 multiple benefits.
DOI: 10.34740/kaggle/dsv/14643496
title: Berita UII
DOI: 10.5061/dryad.tmpg4f4vk
title: Data from: The sex with the reduced sex chromosome dies earlier: a comparison across the tree of life

description: Many taxa show substantial differences in lifespan between the sexes.
 However, these differences are not always in the same direction. In
 mammals, females tend to live longer than males, while in birds, males
 tend to live longer than females. One possible explanation for these
 differences in lifespan is the unguarded X hypothesis, which suggests that
 the reduced or absent chromosome in the heterogametic sex (e.g. the Y
 chromosome in mammals and the W chromosome in birds) exposes recessive
 deleterious mutations on the other sex chromosome. While the unguarded X
 hypothesis is intuitively appealing, it had never been subject to a broad
 test. We compiled male and female longevity data for 229 species spanning
 99 families, 38 orders and eight classes across the tree of life.
 Consistent with the unguarded X hypothesis, a meta-analysis showed that
 the homogametic sex, on average, lives 17.6% longer than the heterogametic
 sex. Surprisingly, we found substantial differences in lifespan dimorphism
 between female heterogametic species (in which the homogametic sex lives
 7.1% longer) and male heterogametic species (in which the homogametic sex
 lives 20.9% longer). Our findings demonstrate the importance of
 considering chromosome morphology in addition to sexual selection and
 environment as potential drivers of sexual dimorphism, and advance our
 fundamental understanding of the mechanisms that shape an organism's
 lifespan.
DOI: 10.5061/dryad.1jwstqjr9
title: The unique spatial ecology of human hunters

description: Human hunters are described as ‘superpredators’ with a unique ecology.
 Chronic Wasting Disease among cervids and African swine fever among wild
 boar are emerging wildlife diseases in Europe with huge economic and
 cultural repercussions. Understanding hunter movements at broad scales has
 implications for how to control their spread. Here we show, based on the
 analysis of the settlement patterns and movements of reindeer (n = 9,685),
 red deer (n = 47,845), moose (n = 60,365), and roe deer (n = 42,530)
 hunters from across Norway (2001-2017), that hunter density was more
 closely linked to human density than prey density, that hunters were
 largely migratory, aggregated with increasing regional prey densities and
 often used dogs. Hunter movements extended across Europe and to other
 continents. Our results provide extensive evidence that the broad-scale
 movements and residency patterns of post-industrial hunters relative to
 their prey differ from those of large carnivores.
description: Data was collected by downloading official statistics from
 Statistics Norway. Details of analysis is provided in
 form of code.
description: Please see readme files
DOI: 10.5061/dryad.51c59zw4q
title: Genetic variation and phenotypic plasticity in circadian rhythms of an armed beetle, Gnatocerus cornutus (Tenebrionidae)

description: Circadian rhythms, their free-running periods and strength of the rhythm
 are often used as indicators of biological clocks, and there is evidence
 that the free-running periods of circadian rhythm are not affected by
 environmental factors like temperature. However, there are few studies of
 environmental effects on the power of rhythms and it is not clear if
 temperature compensation is universal. Additionally, genetic variation and
 phenotypic plasticity in biological clocks are important for understanding
 the evolution of biological rhythm, but genetic and plastic effects are
 rarely investigated. Here, we used 18 isofemale lines (genotypes) of
 Gnatocerus cornutus to assess rhythms of locomotor activity, while also
 testing for temperature effects. We found that total activity and power of
 circadian rhythm were affected by interactions between sex and genotype or
 sex, genotype and temperature, so that while males tended to be more
 active and showed greater increases in activity, this effect varied across
 both genotypes and temperatures. The period of activity only varied by
 genotype and was thus independent of temperature. The complicated
 genotype-sex-environment interactions we recorded stress the importance of
 investigating circadian activity in more integrated ways.
description: To assess circadian rhythm,
 we maintained beetles at 14L10D conditions for more than 20 days in an
 incubator kept at 25<sup>o</sup>C before the measurement of
 locomotor activity, and we then measured the locomotor activity of
 <i>G. cornutus</i> for 10 days in darkness. A beetle from each
 isoline with enough food described above was put in a clear plastic Petri
 dish (30 × 10 mm) in an incubator maintained at
 25<sup>o</sup>C or 29<sup>o</sup>C. The beetles
 develop faster at 29℃ (unpublished observation, TM), and almost
 investigation of the beetle’s behaviour has been conducted under
 25<sup>o</sup>C (Okada et al. 2006; Okada and Miyatake 2009,
 2010), and thus we choose the two temperatures,
 25<sup>o</sup>C and 29<sup>o</sup>C in this
 experiment. The locomotor activity of each individual was monitored using
 an infrared actograph. An infrared light beam was passed through a clear
 Petri dish, and the beam was projected onto a photomicrosensor (E3S-AT11;
 Omron, Kyoto, Japan) that detected all interruptions of the light beam.
 Signals of interruption of the infrared light beam were recorded every 6
 min. Sample size of each isoline is shown in S1 Table.
DOI: 10.5061/dryad.4b8gtht8h
title: Supplemental material for: Morphological phylogenetics evaluated using novel evolutionary simulations

description: Evolutionary inferences require reliable phylogenies. Morphological data
 has traditionally been analysed using maximum parsimony, but recent
 simulation studies have suggested that Bayesian analyses yield more
 accurate trees. This debate is ongoing, in part, because of ambiguity over
 modes of morphological evolution and a lack of appropriate models. Here we
 investigate phylogenetic methods using two novel simulation models – one
 in which morphological characters evolve stochastically along lineages and
 another in which individuals undergo selection. Both models generate
 character data and lineage splitting simultaneously: the resulting trees
 are an emergent property, rather than a fixed parameter. Standard
 consensus methods for Bayesian searches (Mki) yield fewer incorrect nodes
 and quartets than the standard consensus trees recovered using equal
 weighting and implied weighting parsimony searches. Distances between the
 pool of derived trees (most parsimonious or posterior distribution) and
 the true trees – measured using Robinson-Foulds (RF), subtree prune and
 regraft (SPR), and tree bisection reconnection (TBR) metrics – demonstrate
 that this is related to the search strategy and consensus method of each
 technique. The amount and structure of homoplasy in character data differs
 between models. Morphological coherence, which has previously not been
 considered in this context, proves to be a more important factor for
 phylogenetic accuracy than homoplasy. Selection-based models exhibit
 relatively lower homoplasy, lower morphological coherence, and higher
 inaccuracy in inferred trees. Selection is a dominant driver of
 morphological evolution, but we demonstrate that it has a confounding
 effect on numerous character properties which are fundamental to
 phylogenetic inference. We suggest that the current debate should move
 beyond considerations of parsimony versus Bayesian, towards identifying
 modes of morphological evolution and using these to build models for
 probabilistic search methods.
description: Supplemental materials
DOI: 10.15139/s3/hepwk5
title: Data Management and Sharing Plan for: Circuitry- and cell-specific exploration of CB1R positive allosteric modulators in neuroHIV

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.0cfxpnvz3
title: Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

description: In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum
 intermedium), polycrossing is often used to generate novel recombinants
 through each cycle of selection, but it cannot track pollen-parent
 pedigrees and it is unknown how self-incompatibility (SI) genes may limit
 the number of unique crosses obtained. This study investigated the
 potential of using next-generation sequencing to assign paternity and
 identify putative SI loci in IWG. Using a reference population of 380
 individuals made from controlled crosses of 64 parents, paternity was
 assigned with 92% agreement using Cervus software. Using this approach,
 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were
 assigned paternity. Of the 89 pollen parents, 82 (92%) were represented
 with 1633 unique full-sib families representing 42% of all potential
 crosses. The number of progeny per successful pollen parent ranged from 1
 to 123, with number of inflorescences per pollen parent significantly
 correlated to the number of progeny (r = 0.54, p &lt; 0.001).
 Shannon’s diversity index, assessing the total number and representation
 of families, was 7.33 compared to a theoretical maximum of 8.98. To test
 our hypothesis on the impact of SI genes, a genome-wide association study
 of the number of progeny observed from the 89 parents identified genetic
 effects related to non-random mating, including marker loci located near
 putative SI genes. Paternity testing of polycross progeny can impact
 future breeding gains by being incorporated in breeding programs to
 optimize polycross methodology, maintain genetic diversity, and reveal
 genetic architecture of mating patterns.
description: Code and documentation for all analysis provided.  Use README
 file for overview of code and file strucuture.
DOI: 10.5061/dryad.b8gtht78h
title: Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

description: Aim Intraspecific trait variation (ITV) within natural plant communities
 can be large, influencing local ecological processes and dynamics. Here,
 we shed light on how ITV in vegetative and floral traits responds to
 large-scale abiotic and biotic gradients (i.e. climate and species
 richness). Specifically, we tested if associations of ITV with
 temperature, precipitation and species richness were consistent with any
 of from four hypotheses relating to stress-tolerance and competition.
 Furthermore, we estimated the degree of correlation between ITV in
 vegetative and floral traits and how they vary along the gradients.
 Location Global. Time period 1975-2016. Major taxa studied Herbaceous and
 woody plants. Methods We compiled a dataset of 18,112 measurements of the
 absolute extent of ITV (measured as coefficient of variation) in nine
 vegetative and seven floral traits from 2,774 herbaceous and woody species
 at 2,306 locations. Results Large-scale associations between ITV and
 climate were trait-specific and more prominent for vegetative traits,
 especially leaf morphology, than for floral traits. ITV showed pronounced
 associations with climate, with lower ITV values in colder areas and
 higher values in drier areas. The associations of ITV with species
 richness were inconsistent across traits. Species-specific associations
 across gradients were often idiosyncratic and covariation in ITV was
 weaker between vegetative and floral traits than within the two trait
 groups. Main conclusions Our results show that, depending on the traits
 considered, ITV either increased or decreased with climate stress and
 species richness, suggesting that both factors can constrain or enhance
 ITV, which might foster plant-population persistence under stressful
 conditions. Given the species-specific responses and covariation in ITV,
 associations can be hard to predict for traits and species not yet
 studied. We conclude that considering ITV can improve our understanding of
 how plants cope with stressful conditions and environmental change across
 spatial and biological scales.
description: The datasets were collected from databases. Please see the
 supplement material for further details and reference list. Please use the
 original database for access to the data to ensure proper attribution to
 the data collectors.
description: Please see Information file.
DOI: 10.5061/dryad.r4xgxd28b
title: Genetic variance for behavioural ‘predictability’ of stress response

description: Genetic factors underpinning phenotypic variation are required if natural
 selection is to result in adaptive evolution. However, evolutionary and
 behavioural ecologists typically focus on variation among individuals in
 their average trait values, and seek to characterise genetic contributions
 to this. As a result, less attention has been paid to if and how genes
 could contribute towards within-individual variance, or trait
 “predictability”. In fact, phenotypic ‘predictability’ can vary among
 individuals, and emerging evidence from livestock genetics suggests this
 can be due to genetic factors. Here we test this empirically using
 repeated measures of a behavioural stress response trait in a pedigreed
 population of wild-type guppies. We ask (1) whether individuals differ in
 behavioural predictability, and (2) whether this variation is heritable
 and so evolvable under selection. Using statistical methodology from the
 field of quantitative genetics, we find support for both hypotheses and
 also show evidence of a genetic correlation structure between the
 behavioural trait mean and individual predictability. We show that
 investigating sources of variability in trait predictability is
 statistically tractable, and can yield useful biological interpretation.
 We conclude that, if widespread, genetic variance for ‘predictability’
 will have major implications for the evolutionary causes and consequences
 of phenotypic variation. 
description: Please refer to the methodology section for a description of
 our traits listed in the data file.