cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p9b92jh
title: Data from: A hyper arid environment shapes an inverse pattern of the fast–slow plant economics spectrum for above-, but not belowground resource acquisition strategies

description: 1. The fast–slow plant economics spectrum predicts that because of
 evolutionary and biophysical constraints, different plant organs must be
 coordinated to converge in a unique ecological strategy within a continuum
 that shifts from fast to slow resource acquisition and conservation.
 Therefore, along a gradient of aridity, taxa with different strategies
 will be expected to be successful because selection pressures for slow
 resource acquisition become stronger as the environment becomes drier. In
 extremely arid and seasonal environments, however, a slow strategy may
 become disadvantageous because slow traits are costly to maintain.
 Additionally, as the availability of water decreases, selection pressures
 increase, reducing the variation in ecological strategies. 2. Using shrub
 assemblages along an aridity gradient in the Atacama Desert, we test the
 hypothesis that selection pressures imposed by hyper aridity act
 simultaneously on the variation and coordination of trait attributes,
 leading to an inverse pattern in the fast – slow plant economics spectrum,
 where strategies shift from slow to fast as the environment becomes drier.
 3. We established 20 to 22 plots at each of four sites along the gradient
 to estimate plant community structure and functional variation. For all
 species recorded we quantified a set of leaf, stem and, root traits. 4.
 Results revealed an inverse pattern of the fast–slow economics spectrum
 for leaf and stem traits, but not for root traits; that is, as aridity
 further increased, aboveground traits exhibited a shift from a slow to a
 fast strategy with some level of coordination. Belowground traits,
 however, did not shift accordingly with our prediction, rather they showed
 more complex pattern of shift and coordination with aboveground traits
 along the gradient. We also found that trait variation showed an
 idiosyncratic pattern of variation along the gradient, indicating that
 ecological strategies are driven by local processes within sites. 5.
 Synthesis: Our results increase our understanding of the fast–slow plant
 economics spectrum by showing that environmental gradients, as well as
 local process can simultaneously shape different below- and above-ground
 resource acquisition strategies in extremely poor resource environments.
description: Community weighted means
 of plant traitsThe data represents the
 community weighted means for each trait at each plot.dBase_Carvajal et al.
 _JEcol-2018-0167.R2.xlsx
DOI: 10.5061/dryad.47v99r0
title: Data from: Walking crowds on a shaky surface: stable walkers discover Millennium Bridge oscillations with and without pedestrian synchrony

description: Why did the London Millennium Bridge shake when there was a big enough
 crowd walking on it? What features of human walking dynamics when coupled
 to a shaky surface produce such shaking? Here, we use a simple biped model
 capable of walking stably in 3D to examine these questions. We simulate
 multiple such stable bipeds walking simultaneously on a bridge, showing
 that they naturally synchronize under certain conditions, but that
 synchronization is not required to shake the bridge. Under such shaking
 conditions, the simulated walkers increase their step-widths and expend
 more metabolic energy than when the bridge does not shake. We also find
 that such bipeds can walk stably on externally shaken treadmills,
 synchronizing with the treadmill motion for a range of oscillation
 amplitudes and frequencies, sometimes performing net positive work on the
 treadmill. Our simulations illustrate how interactions between (idealized)
 bipeds through the walking surface can produce emergent collective
 behavior that may not be exhibited by just a single biped.
description: ComputerCode_MATLAB_HumanOnBridgeSimulationMATLAB code for simulating multiple humans walking on a shaky bridge.ComputerCode_MATLAB_BridgeSimulation.zip
DOI: 10.5061/dryad.250q1g7
title: Data from: Resistance of corals and coralline algae to ocean acidification: physiological control of calcification under natural pH variability

description: Ocean acidification is a threat to the continued accretion of coral reefs,
 though some undergo daily fluctuations in pH exceeding declines predicted
 by 2100. We test whether exposure to greater pH variability enhances
 resistance to ocean acidification for the coral Goniopora sp. and
 coralline alga Hydrolithon reinboldii from two sites: one with low pH
 variability (&lt; 0.15 units daily; Shell Island), and a site with
 high pH variability (up to 1.4 pH units daily; Tallon Island). We grew
 populations of both species for &gt;100 days under a combination of
 differing pH variability (high/low) and means (ambient pH 8.05/ocean
 acidification pH 7.65). Calcification rates of Goniopora sp. were
 unaffected by the examined variables. Calcification rates of H. reinboldii
 were significantly faster in Tallon than Shell Island individuals, and
 Tallon Island individuals calcified faster in the high variability pH 8.05
 treatment compared to all others. Geochemical proxies for carbonate
 chemistry within the calcifying fluid (cf) of both species indicated that
 only mean seawater pH influenced pHcf. pH treatments had no effect on
 proxies for Ωcf. These limited responses to extreme pH treatments
 demonstrates some calcifying taxa may be capable of maintaining constant
 rates of calcification under ocean acidification by actively modifying
 Ωcf.
description: Calcification Data for
 Cornwall et al 2018Calcification data for
 Cornwall et al 2018. All other data provided in paper
 ESMData
 Cornwall et al 2018.xlsxPhotosynthesis and
 Respiration Cornwall et al 2018
DOI: 10.5061/dryad.qm1n85p
title: Data from: Salamander climbing behavior varies among species and is correlated with community composition

description: Species coexistence is often facilitated by behavioral strategies that
 minimize competition for limited resources. Terrestrial, lungless
 salamanders (genus Plethodon) coexist in predictable assemblages of body
 size guilds, but little is known about the behavioral mechanisms that
 promote such coexistence. Here, we considered the hypothesis that
 Plethodon salamanders use climbing behavior to reduce competitive
 interactions, thereby promoting coexistence through spatial partitioning.
 To explore this hypothesis, we quantified the frequency of climbing
 behavior at field sites where small-bodied (P. cinereus) and large-bodied
 (P. glutinosus) species are always present, but an intermediate-bodied
 species (P. montanus) is either absent, introduced, or native. We observed
 that climbing behavior varied among size guilds so that the smallest
 species climbed most frequently, followed by the intermediate, and then
 the large species. Further, we identified several correlates of climbing
 behavior that may be shaped by intraspecific and interspecific
 competition. Climbing frequency was positively correlated with
 intraspecific competition and negatively correlated with interspecific
 competition in the small species, unrelated to competition in the
 intermediate species, and positively correlated with interspecific
 competition in the large species. Our results suggest that Plethodon size
 guilds might differentially utilize climbing behavior to facilitate
 spatial partitioning in dense populations and communities. Further, we
 show how competition intensity can shape the behavior of cohabitating
 species, and ultimately provide insight into how behavioral plasticity and
 microhabitat partitioning can promote species coexistence.
description: Field observations of
 Plethodon climbing behaviorData was collected in
 the field and the file was created using Microsoft Excel. The column
 headings are as follows: site initials (DCA = Dismal Creek A, DCB = Dismal
 Creek B, HB = Hunter's Branch, WR = Wind Rock, and WSP = War Spur
 Trail); transect (identifier for each 15x3m survey transect), survey
 (survey number, 1-3), date (date of survey), start_time (time of survey
 initiation), stop_time (time of survey completion), species (Plethodon
 species name), count (total individuals observed on a given survey),
 count_climbing (number of individuals found climbing on a given survey),
 count_ground (number of individuals found not climbing or on the ground on
 a given survey), community (denotes whether P. montanus was native,
 introduced, or absent at the specified site), trees (total number of trees
 &gt; 3cm dbh in the transect), understory_mean (mean % understory cover in
 the transect).Mezebish et al. - Salamander
 Survey Data.csv
DOI: 10.5061/dryad.42856
title: Data from: A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo

description: Geographic distributions of phytoplankton species can be defined by events
 on both evolutionary time and shorter scales, e.g., recent climate
 changes. Additionally, modern industrial activity, including the transport
 of live fish and spat for aquaculture and aquatic microorganisms in ship
 ballast water, may aid the spread of phytoplankton. Obtaining a reliable
 marker is key to gaining insight into the phylogeographic history of a
 species. Here, we report a hypervariable mitochondrial gene in the
 cosmopolitan bloom-forming alga, Heterosigma akashiwo. We compared the
 entire mitochondrial genome sequences of seven H. akashiwo strains from
 Japanese and North American coastal waters and identified a hypervariable
 segment. The region codes for a hypothetical protein with no defined
 function, and its variations between Japanese and North American isolates,
 were prominent, while the sequences were more conserved among Japanese
 strains and North American isolates. Comparison of the sequence in
 isolates obtained from different geographical points in the Northern
 Hemisphere revealed that the sequence variations largely correlated with
 latitude and longitude (i.e. Pacific/Atlantic oceans). Our results
 demonstrate the usefulness of the sequence in determining the
 phylogeographic history of H. akashiwo.
description: isolation_by_distanceThe dataset utilized for calculating isolation by distance (Figure 2b)
DOI: 10.5061/dryad.305c3
title: Data from: Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina

description: TelTelomeres usually shorten during an organism’s lifespan and have thus
 been used as an aging and health marker. When telomeres become
 sufficiently short, senescence is induced. The most common method of
 restoring telomere length is via telomerase reverse transcriptase
 activity, highly expressed during embryogenesis. However, although asexual
 reproduction from adult tissues has an important role in the life cycles
 of certain species, its effect on the aging and fitness of wild
 populations, as well as its implications for the long-term survival of
 populations with limited genetic variation, is largely unknown. Here we
 compare relative telomere length of 58 individuals from four populations
 of the asexually reproducing starfish Coscinasterias tenuispina.
 Additionally, 12 individuals were used to compare telomere lengths in
 regenerating and non-regenerating arms, in two different tissues (tube
 feet and pyloric cecum). The level of clonality was assessed by genotyping
 the populations based on 12 specific microsatellite loci and relative
 telomere length was measured via quantitative PCR. The results revealed
 significantly longer telomeres in Mediterranean populations than Atlantic
 ones as demonstrated by the Kruskal–Wallis test (K=24.17, significant
 value: P-value&lt;0.001), with the former also characterized by higher
 levels of clonality derived from asexual reproduction. Telomeres were
 furthermore significantly longer in regenerating arms than in
 non-regenerating arms within individuals (pyloric cecum tissue:
 Mann–Whitney test, V=299, P-value&lt;10−6; and tube feet tissue
 Student's t=2.28, P-value=0.029). Our study suggests that one of the
 mechanisms responsible for the long-term somatic maintenance and
 persistence of clonal populations is telomere elongation.
description: Telomere measurements
 and genotypesGenotypes and telomere
 measurements from all the individuals are provided in two excel sheets. In
 the first sheet, named "Population data", reports the arm
 length, ct. values and genotypes of all individuals. Finally, the second
 sheet, reports the ct. values from different tissues in regenerating and
 non-regenerating arms.Hdy_Garcia-Cisneros
 2015.xls
DOI: 10.5061/dryad.jb235
title: Data from: Human punishment is not primarily motivated by inequality

description: Previous theorizing about punishment has suggested that humans desire to
 punish inequality per se. However, the research supporting such an
 interpretation contains important methodological confounds. The main
 objective of the current experiment was to remove those confounds in order
 to test whether generating inequality per se is punished. Participants
 were recruited from an online market to take part in a wealth-alteration
 game with an ostensible second player. The participants were given an
 option to deduct from the other player’s payment as punishment for their
 behavior during the game. The results suggest that human punishment does
 not appear to be motivated by inequality per se, as inequality that was
 generated without inflicting costs on others was not reliably punished.
 Instead, punishment seems to respond primarily to the infliction of costs,
 with inequality only becoming relevant as a secondary input for punishment
 decisions. The theoretical significance of this finding is discussed in
 the context of its possible adaptive value.
description: InequalityDataCleaned
DOI: 10.5061/dryad.nh427
title: Data from: Experimental warming increases herbivory by leaf-chewing insects in an alpine plant community

description: Climate warming is predicted to affect species and trophic interactions
 worldwide, and alpine ecosystems are expected to be especially sensitive
 to changes. In this study, we used two ongoing climate warming (open-top
 chambers) experiments at Finse, southern Norway, to examine whether
 warming had an effect on herbivory by leaf-chewing insects in an alpine
 Dryas heath community. We recorded feeding marks on the most common
 vascular plant species in warmed and control plots at two experimental
 sites at different elevations and carried out a brief inventory of insect
 herbivores. Experimental warming increased herbivory on Dryas octopetala
 and Bistorta vivipara. Dryas octopetala also experienced increased
 herbivory at the lower and warmer site, indicating an overall positive
 effect of warming, whereas B. vivipara experienced an increased herbivory
 at the colder and higher site indicating a mixed effect of warming. The
 Lepidoptera Zygaena exulans and Sympistis nigrita were the two most common
 leaf-chewing insects in the Dryas heath. Based on the observed patterns of
 herbivory, the insects life cycles and feeding preferences, we argue that
 Z. exulans is the most important herbivore on B. vivipara, and S. nigrita
 the most important herbivore on D. octopetala. We conclude that if the
 degree of insect herbivory increases in a warmer world, as suggested by
 this study and others, complex interactions between plants, insects, and
 site-specific conditions make it hard to predict overall effects on plant
 communities.
description: Feedingmarks on Dryas
 octopetala and Bistorta vivipara inside and otside OTCs at Finse,
 NorwayThe data is based on
 field observations in two summer periods. The file consists of 3
 datasheets: 1. used in table 1 in publication with feeding marks on
 Bistorta and Dryas. Feeding index as defined in publications 2. feeding
 marks on other common plant species 3. precentage of each leaf removed
 (table 2 in publication).HerbivoryFinse.xlsx
DOI: 10.5061/dryad.5h17h
title: Data from: Genetic basis of priority effects: insights from nectar yeast

description: Priority effects, in which the order of species arrival dictates community
 assembly, can have a major influence on species diversity, but the genetic
 basis of priority effects remains unknown. Here, we suggest that nitrogen
 scavenging genes previously considered responsible for starvation
 avoidance may drive priority effects by causing rapid resource depletion.
 Using single-molecule sequencing, we de novo assembled the genome of the
 nectar-colonizing yeast, Metschnikowia reukaufii, across eight scaffolds
 and complete mitochondrion, with gap-free coverage over gene spaces. We
 found a high rate of tandem gene duplication in this genome, enriched for
 nitrogen metabolism and transport. Both high-capacity amino acid
 importers, GAP1 and PUT4, present as tandem gene arrays, were highly
 expressed in synthetic nectar and regulated by the availability and
 quality of amino acids. In experiments with competitive nectar yeast,
 Candida rancensis, amino acid addition alleviated suppression of C.
 rancensis by early arrival of M. reukaufii, corroborating that amino acid
 scavenging may contribute to priority effects. Because niche pre-emption
 via rapid resource depletion may underlie priority effects in a broad
 range of microbial, plant and animal communities, nutrient scavenging
 genes like the ones we considered here may be broadly relevant to
 understanding priority effects.
description: Mreukaufii amino acid
 transporters aligned with Clavispora lusitaniae and Saccharomyces
 cerevisiae homologsAlignment file created
 in Geneious 8.0 using Blosum62 cost matrixMreukaufii_transporters.nexMreukaufii_transporters_GAP1&PUT4 aligned to homologs from Clavispora lusitaniae and Saccharomyces cerevisiaeProtein sequence alignment created in Geneious 8.0 using the BLOSUM62 cost matrix and manually curated.Mreukaufii_transporters_alignment.nex
DOI: 10.5061/dryad.367f16t
title: Data from: Mitochondria and Wolbachia titers are positively correlated during maternal transmission

description: Mothers provide their offspring with symbionts. Maternally transmitted,
 intracellular symbionts must disperse from mother to offspring with other
 cytoplasmic elements, like mitochondria. Here, we investigated how the
 intracellular symbiont Wolbachia interacts with mitochondria during
 maternal transmission. Mitochondria and Wolbachia may interact
 antagonistically and compete as each population tries to ensure its own
 evolutionary success. Alternatively, mitochondria and Wolbachia may
 cooperate as both benefit from ensuring the fitness of the mother. We
 characterized the relationship between mitochondria and Wolbachia titers
 in ovaries of D. melanogaster. We found that mitochondria and Wolbachia
 titers are positively correlated in common laboratory genotypes of D.
 melanogaster. We attempted to perturb this covariation through the
 introduction of Wolbachia variants that colonize at different titers. We
 also attempted to perturb the covariation through manipulating the female
 reproductive tract to disrupt maternal transmission. Finally, we also
 attempted to disrupt the covariation by knocking down gene expression for
 two loci involved in mitochondrial metabolism: NADH dehydrogenase and a
 mitochondrial transporter. Overall, we find that mitochondria and
 Wolbachia titers are commonly positively correlated, but this positive
 covariation is disrupted at high titers of Wolbachia. Our results suggest
 that mitochondria and Wolbachia have likely evolved mechanisms to stably
 coexist, but the competitive dynamics change at high Wolbachia titers. We
 provide future directions to better understand how their interaction
 influences the maintenance of the symbiosis.
description: fig1a_data_mitosmitochondria titers in multiple lab genotypesfig2_data_mitowolsdata comparing mitochondria and wolbachia titers in wMel genotypes where wolbachia genotype determines wolbachia titerfig1_data_labgenosmitochondria and wolbachia titers in common lab genotypesfig3_data_tripmitochondria and wolbachia titers in TRiP knockdown experimentsfig3a_data_tripwesternswolbachia abundance as measured through Western blot in TRiP knockdown experimentsfig4a_data_intensitygermwolbachia abundance from microscopy measured through fluorescence intensity in germaria from TRiP knockdownfig4b_data_intensityearlywolbachia abundance from microscopy measured through fluorescence intensity in early oogenesis from TRiP knockdownfig4c_data_intensitymidwolbachia abundance from microscopy measured through fluorescence intensity in mid oogenesis from TRiP knockdownfig5_data_mitokdwolbachia and mitochondria titers in mito knockdown experimentssuppfig8_data_triprelexpdata for relative expression of mitochondria and wolbachia
DOI: 10.5061/dryad.7mf4k
title: Data from: No evidence that sex and transposable elements drive genome size variation in evening primroses

description: Genome size varies dramatically across species, but despite an abundance
 of attention there is little agreement on the relative contributions of
 selective and neutral processes in governing this variation. The rate of
 sex can potentially play an important role in genome size evolution
 because of its effect on the efficacy of selection and transmission of
 transposable elements. Here, we used a phylogenetic comparative approach
 and whole genome sequencing to investigate the contribution of sex and
 transposable element content to genome size variation in the evening
 primrose (Oenothera) genus. We determined genome size using flow cytometry
 for 30 species that vary in genetic system and find that variation in
 sexual/asexual reproduction cannot explain the almost two-fold variation
 in genome size. Moreover, using whole genome sequences of three species of
 varying genome sizes and reproductive system, we found that genome size
 was not associated with transposable element abundance; instead the larger
 genomes had a higher abundance of simple sequence repeats. Although it has
 long been clear that sexual reproduction may affect various aspects of
 genome evolution in general and transposable element evolution in
 particular, it does not appear to have played a major role in genome size
 evolution in the evening primroses.
description: Supplementary Table
 1Information about
 samples used for Illumina sequecning and flow
 cytometry.Supplementary Table
 2C-value estimates as
 determined by flow cytometry.