cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.00s51
title: Data from: Asymmetry in pay-off predicts how familiar individuals respond to one another

description: Familiarity influences individual decision-making in many vertebrate
 species. Here, we propose that familiarity modulates behaviour to
 different extents depending on the social context of the interaction.
 Specifically, the more that one player stands to gain relative to the
 other, the less important familiarity will be in influencing their
 responses to one another. We test this prediction using pairs of male
 guppies (Poecilia reticulata) in three competitive scenarios of increasing
 asymmetry in outcome to the two players: schooling under potential threat
 (similar outcomes), competing for a defensible food source (some
 asymmetry) and competing for a receptive female (strongly asymmetrical
 outcomes). Males show a graded response as asymmetry increases, with
 familiarity producing marked behavioural differences under potential
 threat, minor changes when competing for food, but none at all in
 competition for mating opportunities. This suggests that mutualistic
 benefits can arise as a by-product of selfish behaviour, supporting the
 role of pseudo-reciprocity in the evolution of cooperation.
description: Context-dependent male
 familiarity dataThis file contains the
 data for all three experiments in the paper: behaviour under predation
 threat, competing for food and competing for mates. Each experiment is in
 a separate tab of an Excel file. Column heading should be clear with
 reference to the manuscript. All data was collected experimentally using a
 lab-bred population.ContextDependentMaleFamiliarity.xls
DOI: 10.5061/dryad.8k01q
title: Data from: Evolutionary reversals of antibiotic resistance in experimental populations of Pseudomonas aeruginosa

description: Antibiotic resistance mutations are accompanied by a fitness cost, and two
 mechanisms allow bacteria to adapt to this cost once antibiotic use is
 halted. First, it is possible for resistance to revert; second, it is
 possible for bacteria to adapt to the cost of resistance by compensatory
 mutations. Unfortunately, reversion to antibiotic sensitivity is rare, but
 the underlying factors that prevent reversion remain obscure. Here, we
 directly study the evolutionary dynamics of reversion by experimentally
 mimicking reversion mutations—sensitives—in populations of
 rifampicin-resistant Pseudomonas aeruginosa. We show that, in our
 populations, most sensitives are lost due to genetic drift when they are
 rare. However, clonal interference from lineages carrying compensatory
 mutations causes a dramatic increase in the time to fixation of sensitives
 that escape genetic drift, and mutations surpassing the sensitives’
 fitness are capable of driving transiently common sensitive lineages to
 extinction. Crucially, we show that the constraints on reversion arising
 from clonal interference are determined by the potential for compensatory
 adaptation of the resistant population. Although the cost of resistance
 provides the incentive for reversion, our study demonstrates that both the
 cost of resistance and the intrinsic evolvability of resistant populations
 interact to determine the rate and likelihood of reversion.
description: Data from Figures
 1-4XLS File produced with
 LibreOffice Calc 4.0.2.2. Data were collected in a laboratory experimental
 evolution experiment. Tab1: Presence/absence data for sensitive in the
 presence of +P518 and S536F. Tab 2: Fixation events of sensitives in the
 presence of +P518 and S536F. Tab 3: Frequency of sensitives in the
 presence of +P518 and S536F. Tab 4: Competitive fitness of compensated
 +P518 and S536F lineages evolved in the absence of the sensitive
 competitor.data-all-figures.xls
DOI: 10.5061/dryad.7992
title: Data from: Isolation by time and habitat and coexistence of distinct host races of the common cuckoo

description: Isolation by time occurs when different populations of a single species
 reproduce at different times and thereby reduce the probability of
 interbreeding, potentially causing divergent adaptation to timing of
 reproduction, eventually resulting in ecological species separated by
 timing of reproduction. We analyzed extensive data on timing of
 reproduction by different host races of the common cuckoo Cuculus canorus
 that is an obligate brood parasite laying eggs in the nests of many
 different species of passerine birds. Because different hosts breed at
 different times, specific host races of cuckoos have adapted to specific
 hosts by laying eggs when nests of these hosts are available, and such
 divergence may be further exaggerated by differences in timing of breeding
 among host races with similar habitat requirements. Host species accounted
 for a quarter of the variance in timing of breeding by the cuckoo. Common
 cuckoos reproduced at a similar, but narrower subset of dates as did
 possible hosts, showing that only a fraction of hosts with specific
 breeding dates were parasitized. Common cuckoo eggs laid in the
 'right' kind of nests, phenotypically matching the eggs of the
 host, were laid later during the season than cuckoo eggs laid in the
 'wrong' kind of nests where the eggs did not mimic those of the
 host. Pairs of sympatric cuckoo host races differed more in timing of
 breeding than pairs of allopatric host races, and pairs of cuckoo host
 races with similar breeding habitat differed more in breeding date than
 pairs of cuckoo host races with dissimilar habitat, as expected from
 reproductive character displacement. These findings are consistent with
 cuckoo host races being isolated by timing of breeding and habitat.
description: TableMean Julian (SE)
 breeding date for cuckoos exploiting a given host and mean Julian (SE)
 breeding date for the same host species. See paper for further
 details.
DOI: 10.5061/dryad.pg632hc
title: Data from: Minimal effects on genetic structuring of a fungus-dwelling saproxylic beetle after recolonization of a restored forest

description: 1. Habitat restoration aims to improve local habitat conditions for
 threatened species. While such restorations are widespread, rigorous
 evaluations of their success are rare. This is especially true of those
 considering species dynamics. Increasingly, deadwood is a target for
 forest restoration as many species directly and indirectly depend on this
 resource. 2. In a broadleaf forest in southern Germany, we explored the
 effect of landscape-wide deadwood restoration on the population genetic
 structure of the specialist fungus-dwelling saproxylic beetle Bolitophagus
 reticulatus. Before 2003, the northern area of this forest was intensively
 logged for more than half a century, while the southern part was less
 intensively managed. This drove populations of the host fungus Fomes
 fomentarius, and consequently the beetle, to local extinction in the
 northern part. Only after the first decade of restoration were both the
 fungus and its beetles present across all areas of the forest. 3. Using 17
 newly-developed microsatellite loci, we show that these beetles exhibit
 population genetic structuring, mainly influenced by the north-south
 divide. However, the low degree of isolation-by-distance, and the low
 relatedness of beetles collected from the same trees or fungus, shows that
 strong dispersal ability is facilitating the recolonization of these
 forests on the scale of 10s km. In another ten years it is likely that the
 population will show even less genetic structuring. 4. Synthesis and
 applications. Through the recolonization of the fungus (Fomes fomentarius)
 and the fungus-dwelling beetle (Bolitophagus reticulatus) after deadwood
 restoration, we demonstrate that, while there are many discussions on the
 optimal spatial distribution of deadwood, just the presence of deadwood
 can be sufficient to enable recolonizations of specific species. As long
 as some relict populations of these species are embedded in a once
 intensively-managed forest, increased deadwood (amount and diversity)
 anywhere will benefit recolonization of the habitat. However, increasing
 deadwood diversity should also be encouraged to benefit even more species.
description: Zytynska et al.
 Bolitophagus dataBolitophagus reticulatus
 beetles were collected from Fomes fomentarius fungal bodies, in the
 ‘Steigerwald’ forest area in southern Germany (Bavaria) (N 49° 50' 53
 E 10° 29' 41), 2014-2015, across the three different scales
 (within-fungi, within-tree, and among trees). Data gives geographic
 location, tree and fungi ID and the multi-locus genotype of each beetles
 as identified from 17 newly-developed microsatellite
 loci.
DOI: 10.5281/zenodo.18001267
title: Foraminiferal and isotopic tracers of productivity off Cape Blanc, NW Africa

description: A high-resolution dataset of planktonic and benthic foraminiferal abundance and stable carbon and oxygen isotopes (δ13C, δ18O) from the upper 10 cm of 12 MUC cores along two transects, spanning from ~100 to ~3500 m water depth offshore Cape Blanc, North Atlantic Ocean. Planktonic and benthic foraminiferal abundance data are in number of specimen (test)/sample, while δ13C, and δ18O data collected from shallow-dwelling Globigerinoides ruber, epibenthic Cibicidoides wuellerstorfi and inbenthic Uvigerina peregrina tests are expressed in ‰, VPDB.
DOI: 10.5281/zenodo.18001268
title: Foraminiferal and isotopic tracers of productivity off Cape Blanc, NW Africa

description: A high-resolution dataset of planktonic and benthic foraminiferal abundance and stable carbon and oxygen isotopes (δ13C, δ18O) from the upper 10 cm of 12 MUC cores along two transects, spanning from ~100 to ~3500 m water depth offshore Cape Blanc, North Atlantic Ocean. Planktonic and benthic foraminiferal abundance data are in number of specimen (test)/sample, while δ13C, and δ18O data collected from shallow-dwelling Globigerinoides ruber, epibenthic Cibicidoides wuellerstorfi and inbenthic Uvigerina peregrina tests are expressed in ‰, VPDB.
DOI: 10.5061/dryad.9d9s3
title: Data from: Locomotor endurance predicts differences in realized dispersal between sympatric sexual and unisexual salamanders

description: Dispersal is the central mechanism that determines connectivity between
 populations yet few studies connect the mechanisms of movement with
 realized dispersal in natural populations. To make such a link, we
 assessed how physiological variation among individuals predicted dispersal
 in natural populations of unisexual (all-female) and sexual Ambystoma
 salamanders on the same fragmented landscape in Ohio. Specifically, we
 assessed variation in a trait that influences long-distance animal
 movement (locomotor endurance) and determined whether variation in
 endurance matched patterns of realized dispersal assessed using genetic
 assignment tests. A possible mechanism for why unisexuals would have lower
 locomotor endurance than a sympatric sexual species (Ambystoma texanum) is
 the potential energetic cost of evolutionarily mismatched mitochondrial
 and nuclear genomes within polyploid unisexuals. We found that sexuals
 walked four times farther than unisexuals during treadmill endurance
 trials that mimic the locomotor endurance required for dispersal. We then
 applied landscape genetic methods to identify dispersed adults and
 quantify realized dispersal. We show that the differences in locomotor
 endurance between unisexual and sexual salamanders scale to realized
 dispersal: dispersing sexual individuals travelled approximately twice the
 distance between presumed natal wetlands and the site of capture compared
 to dispersing unisexuals. This study links variation in individual
 performance in terms of endurance with realized dispersal in the field and
 suggests a potential mechanism (physiological limitation due to
 mitonuclear mismatch) for the reduced endurance of unisexual individuals
 relative to sexual individuals although we discuss other possible
 explanations. The differences in dispersal between these two types of
 salamanders also informs our understanding of sexual/unisexual coexistence
 by suggesting that unisexuals are at a competitive disadvantage in terms
 of colonization ability under a extinction-colonization model of
 coexistence.
description: Ambystoma_DAPC_DryadR script performing DAPC genetic clustering and assignment tests. Requires separate input files for A. texanum and unisexual Ambystoma.Ambystoma_Genetic DataCompressed file consisting of separate R input files for Ambystoma texanum and unisexual Ambystoma. The data for each group is included as txt input files associated with the included R script and CSV files that include group membership as a separate column.
DOI: 10.5061/dryad.v240b
title: Data from: Leaf traits of African woody savanna species across climate and soil fertility gradients: evidence for conservative vs. acquisitive resource use strategies

description: 1. Establishing trade-offs among traits and the degree to which they
 co-vary along environmental gradients has become a key focal point in the
 effort to develop community ecology into a predictive science. While there
 is evidence for these relationships across global datasets, they are often
 too broad in scale, and do not consider the particularities of local to
 regional species pools. This decreases their usefulness for developing
 predictive models at scales relevant for conservation and management. 2.
 We tested for trade-offs between traits and relationships with
 environmental gradients in trees and shrubs sampled across southern
 African savannas and explored evidence for acquisitive vs. conservative
 resource use strategies using a phylogenetically explicit approach. 3. We
 found a distinct trade-off between two major poles of specialization
 indicative of acquisitive (high leaf nitrogen concentration (LNC), leaf
 phosphorus concentration (LPC), leaf N:P, specific leaf area (SLA) and
 average leaf area (ALA)) and conservative resource use strategies (high
 leaf carbon to nitrogen ratios (C:N), tensile strength (TS) and leaf dry
 matter content (LDMC)). Although we found that trait variance and species
 occurrence were constrained by phylogeny, phylogenetically informed
 analyses did not contradict non-phylogenetic analyses, strengthening
 relationships in most cases. 4. The high intra-site trait variability and
 weak relationships with soils and climate may in part be explained by the
 high levels of deciduousness and disturbance (i.e. fire and herbivory)
 inherent in African savannas. 5. Synthesis: The relationships between
 traits and between traits and environmental gradients were far weaker
 than, and often contradictory to, broad scale studies that compare these
 relationships across biomes and growth forms, cautioning against making
 generalizations about relationships at specific sites based on broad scale
 analyses.
description: Wigley_etal_2016_JE_dataLeaf trait data for the dominant woody species found at 16 sites in Southern Africa, measures of soil fertility and climate are also provided for each site.
DOI: 10.5061/dryad.v8g60
title: Data from: Heritability of symbiont density reveals distinct regulatory mechanisms in a tripartite symbiosis

description: Beneficial eukaryotic–bacterial partnerships are integral to animal and
 plant evolution. Understanding the density regulation mechanisms behind
 bacterial symbiosis is essential to elucidating the functional balance
 between hosts and symbionts. Citrus mealybugs, Planococcus citri (Risso),
 present an excellent model system for investigating the mechanisms of
 symbiont density regulation. They contain two obligate nutritional
 symbionts, Moranella endobia, which resides inside Tremblaya princeps,
 which has been maternally transmitted for 100–200 million years. We
 investigate whether host genotype may influence symbiont density by
 crossing mealybugs from two inbred laboratory-reared populations that
 differ substantially in their symbiont density to create hybrids. The
 density of the M. endobia symbiont in the hybrid hosts matched that of the
 maternal parent population, in keeping with density being determined
 either by the symbiont or the maternal genotype. However, the density of
 the T. princeps symbiont was influenced by the paternal host genotype. The
 greater dependency of T. princeps on its host may be due to its highly
 reduced genome. The decoupling of T. princeps and M. endobia densities, in
 spite of their intimate association, suggests that distinct regulatory
 mechanisms can be at work in symbiotic partnerships, even when they are
 obligate and mutualistic.
description: Supporting
 informationThe mean CT values of
 the host control P. citri 28S rDNA gene, target M. endobia 16S and 23S
 rDNA and target T. princeps GroEL gene from individual adult female P.
 citri from the populations A (n = 39) and B (n = 40), and from A♀B♂ and
 A♂B♀ (20 pooled offspring per mother, n = 28 mothers for A♀B♂, n = 29
 mothers for A♂B♀).J. Parkinson Supporting
 information.xlsx
DOI: 10.5061/dryad.rk26g0n
title: Data from: Vegetation connectivity increases ant activity and potential for ant-provided biocontrol services in a tropical agroforest

description: In natural and managed systems, connections between trees are important
 structural resources for arboreal ant communities with ecosystem-level
 effects. However, ongoing agricultural intensification in agroforestry
 systems, which reduces shade trees and connectivity between trees and crop
 plants, may hinder ant recruitment rates to resources and pest control
 services provided by ants. We examined whether increasing connectivity
 between coffee plants and shade trees in coffee plantations increases ant
 activity and enhances biological control of the coffee berry borer, the
 most devastating insect pest of coffee. Further, we examined whether
 artificial connections buffer against the loss of vegetation connectivity
 in coffee plants located at larger distances from the nesting tree. We
 used string to connect Inga micheliana shade trees containing Azteca
 sericeasur ant nests to coffee plants to compare ant activity before and
 after placement of the strings, and measured borer removal by ants on
 coffee plants with and without strings. Ant activity significantly
 increased after the addition of strings on connected plants, but not on
 control plants. Borer removal by ants was also three times higher on
 connected plants after string placement. Greater distance from the nesting
 tree negatively influenced ant activity on control coffee plants, but not
 on connected plants, suggesting that connections between coffee plants and
 nest trees could potentially compensate for the negative effects that
 larger distances pose on ant activity. Our study shows that favoring
 connectivity at the local scale, by artificially adding connections,
 promotes ant activity and may increase pest removal in agroecosystems.
description: All_data_R_ants-connectivityCSV file containing ant activity on coffee plants and CBB removal before and after the placement of strings. Rows are plants. Each site contains 6 plants. trans columns refer to transformed data from densiometer. This dataset does not contain data from ant activity on the trees.All_data_R_revisions.csv
DOI: 10.15468/dl.94fnm8
title: Occurrence Download

description: A dataset containing 395 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Alpinia hainanensis, Alpinia katsumadai)"
 ]
}

 The dataset includes 395 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001232-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hp370m2
title: Data from: Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase

description: While synonymous mutations were long thought to be without phenotypic
 consequences, there is growing evidence they can affect gene expression,
 protein folding and ultimately the fitness of an organism. In only a few
 cases have the mechanisms by which synonymous mutations affect the
 phenotype been elucidated. We previously identified 48 mutations in TEM-1
 β-lactamase that increased resistance of Escherichia coli to cefotaxime,
 10 of which were synonymous. To better understand the molecular mechanisms
 underlying the beneficial effect of synonymous mutations, we made a series
 of measurements for a panel containing the 10 synonymous together with 10
 non-synonymous mutations as a reference. Whereas messenger levels were
 unaffected, we found that total and functional TEM protein levels were
 higher for 5 out of 10 synonymous mutations. These observations suggest
 that some of these mutations act on translation or a downstream process.
 Similar effects were observed for some small-benefit non-synonymous
 mutations, suggesting a similar causal mechanism. For the synonymous
 mutations, we found that the cost of resistance scales with TEM protein
 levels. A resistance landscape for four synonymous mutations revealed
 strong epistasis: None of the combinations of mutations exceeded the
 resistance of the largest-effect mutation and there were synthetically
 neutral combinations. By considering combined effects of these mutations,
 we could infer that functional TEM protein level is a multi-dimensional
 phenotype. These results suggest that synonymous mutations may have
 beneficial effects by increasing the expression of an enzyme with low
 substrate activity, which may be realized via multiple, yet unknown,
 post-transcriptional mechanisms.
description: Readme text
 fileReadme text file
 providing an overview of the data, and descriptions of what the columns in
 *.csv files contain.Data_FilesZip file containing all 11 data files: 10 *.csv files and 1 *.R.txt file. Please refer to the Readme.txt file (not in the zip file) for explanation.
DOI: 10.5061/dryad.qt2qb
title: Data from: Mountain pine beetle seasonal timing and constraints to bivoltinism: a comment on Mitton and Ferrenberg (2012)

description: Mountain pine beetle tree colonization typically occurs in July and
 August, with completion of a generation one (univoltinism) or two
 (semivoltinism) years later. In a 2012 publication, Mitton and Ferrenberg
 suggested that climate change resulted in an unprecedented generation
 between June and September (a summer generation), with a concomitant shift
 to two generations in one year (bivoltinism). Although summer generations
 are not uncommon in this species, completion of a second generation across
 winter, between September and June, would be required for bivoltinism, a
 phenomenon not previously observed. Mitton and Ferrenberg showed that a
 summer generation can occur, but they failed to adequately track cohorts
 and provided no compelling evidence for bivoltinism. We demonstrate that a
 winter generation—and hence bivoltinism—would have been physiologically
 impossible at the high-elevation site used in Mitton and Ferrenberg due to
 lower thermal developmental thresholds. The mountain pine beetle is indeed
 being influenced by climate change. To address the challenges of future
 population outbreaks of this significant tree mortality agent, however, it
 is imperative to consider evolved, thermally dependent traits that serve
 to maintain seasonality.
description: Development time
 dataDevelopment time data of
 Dendroctonus ponderosae lifestages at several constant
 temperaturestimedata.xlsx