cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gh337n5
title: Data from: Life‐history correlations change under coinfection leading to higher pathogen load

description: The ability of a parasite strain to establish and grow on its host may be
 drastically altered by simultaneous infection by other parasite strains.
 However, we still lack an understanding of how life‐history allocations
 may change under coinfection, although life‐history correlations are a
 critical mechanism restricting the evolutionary potential and
 epidemiological dynamics of pathogens. Here, we study how life‐history
 stages and their correlations change in the obligate fungal pathogen
 Podosphaera plantaginis under single infection and coinfection scenarios.
 We find increased pathogen loads under coinfection, but this is not
 explained by an enhanced performance at any of the life‐history stages
 that constitute infections. Instead, we show that under coinfection the
 correlation between timing of sporulation and final pathogen load becomes
 positive. The changes in pathogen life‐history allocations leading to more
 severe infections under coinfection can have far‐reaching epidemiological
 consequences, as well as implication for our understanding of the
 evolution of virulence.
description: Laine&Makinen_EvolLett_DataLife-hitory stages of Podosphaera plantaginis
DOI: 10.5061/dryad.44894
title: Data from: Trapped within the city: Integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization

description: Urbanization is a severe form of habitat fragmentation that can cause many
 species to be locally extirpated and many others to become trapped and
 isolated within an urban matrix. The role of drift in reducing genetic
 diversity and increasing genetic differentiation is well recognized in
 urban populations. However, explicit incorporation and analysis of the
 demographic and temporal factors promoting drift in urban environments are
 poorly studied. Here, we genotyped 15 microsatellites in 320 fire
 salamanders from the historical city of Oviedo (Est. 8th century) to
 assess the effects of time since isolation, demographic history
 (historical effective population size; Ne) and patch size on genetic
 diversity, population structure and contemporary Ne. Our results indicate
 that urban populations of fire salamanders are highly differentiated, most
 likely due to the recent Ne declines, as calculated in coalescence
 analyses, concomitant with the urban development of Oviedo. However,
 urbanization only caused a small loss of genetic diversity. Regression
 modelling showed that patch size was positively associated with
 contemporary Ne, while we found only moderate support for the effects of
 demographic history when excluding populations with unresolved history.
 This highlights the interplay between different factors in determining
 current genetic diversity and structure. Overall, the results of our study
 on urban populations of fire salamanders provide some of the very first
 insights into the mechanisms affecting changes in genetic diversity and
 population differentiation via drift in urban environments, a crucial
 subject in a world where increasing urbanization is forecasted.
description: Lourenco_etal_MolEcol_genotype_databaseDataset containing genotypes of 15 microsatellite loci genotyped in 16 populations of Salamandra salamandra in Oviedo.
DOI: 10.5061/dryad.q0qq3
title: Data from: Food supplementation and predation risk in harsh climate: interactive effects on abundance and body condition of tit species

description: Food availability and predation risk can have drastic impacts on animal
 behaviour and populations. The tradeoff between foraging and predator
 avoidance is crucial for animal survival and will strongly affect
 individual body mass, since large fat reserves are beneficial to reduce
 starvation but may increase predation risk. However, two-factor
 experiments simultaneously investigating the interactive effects of food
 and predation risk, are still rare. We studied the effects of food
 supplementation and natural predation risk imposed by pygmy owls
 Glaucidium passerinum on the abundance and fat reserves of tit species in
 boreal forests of north Europe, from January to March in 2012 and in 2013.
 Food supplementation increased the number of individuals present in a
 given forest patch, whereas the level of predation risk had no clear
 impact on the abundance of tit species. The stronger impact of food supply
 respect to predation risk could be the consequence of the harsh winter
 conditions in north Europe, with constant below-zero temperatures and only
 few (5-7 h) daylight hours available for foraging. Predation risk did not
 have obvious effects on tit abundance but influenced food consumption and,
 together with food supplementation, affected the deposition of
 subcutaneous fat in great tits Parus major. High owl predation risk had
 detrimental effects on body fat reserves, which may reduce over-winter
 survival, but the costs imposed by pygmy owl risk were compensated when
 food was supplemented. The starvation–predation tradeoff faced by great
 tits in winter may thus be mediated through variation in body fat
 reserves. In small species living in harsh environment, this tradeoff
 appeared thus to be biased towards avoidance of starvation, at the cost of
 increasing predation risk.
description: Data_Tit abundance and
 conditionData on tit abundance
 (both census and mist net trapping data for all tit species combined and
 species-specific data), great tit condition (scaled body mass and fat
 score) and both oat and fat consumption. See the ReadMe file for
 details.
DOI: 10.5061/dryad.8487r
title: Data from: Predator identity influences metacommunity assembly

description: 1.Predation is among the most important biotic factors influencing natural
 communities, yet we have a rather rudimentary understanding of its role in
 modulating metacommunity assembly. 2.We experimentally examined the
 effects of two different predators (a generalist and a specialist) on
 metacommunity assembly, using protist microcosm metacommunities that
 varied in predator identity, dispersal among local communities, and the
 history of species colonization into local communities. 3.Generalist
 predation resulted in reduced α diversity and increased β diversity
 irrespective of dispersal, likely due to predation-induced stochastic
 extinction of different prey species in different local communities.
 Dispersal, however, induced source-sink dynamics in the presence of
 specialist predators, resulting in higher α diversity and marginally lower
 β diversity. 4.These results demonstrate the distinct effects of different
 predators on prey metacommunity assembly, emphasizing the need to explore
 the role of predator diet breadth in structuring metacommunities.
description: Population Densities of
 Protists in Microcosms under varying assembly history, dispersal, and
 predator treatmentsPopulation densities of
 protists in microcosms (number of individuals/ml). Microcosms varied in
 assembly history, predator identity, and dispersal with each
 history/predator/dispersal treatment repeated three times. Predator and
 dispersal key included on spreadsheet. Assembly history key can be found
 in supplementary materials of article. Note that Chilomones were added to
 all microcosms at the beginning of the experiment as a food source for the
 predator, and thus, not part or the assembly history
 treatment.metacommunity_JAE_data.csv
DOI: 10.5061/dryad.9t405v8
title: Data from: Phoretic dispersal influences parasite population genetic structure

description: Dispersal is a fundamental component of the life history of most species.
 Dispersal influences fitness, population dynamics, gene flow, genetic
 drift, and population genetic structure. Even small differences in
 dispersal can alter ecological interactions and trigger an evolutionary
 cascade. Linking such ecological processes with evolutionary patterns is
 difficult, but can be done in the proper comparative context. Here we
 investigate how differences in phoretic dispersal influence the population
 genetic structure of two different parasites of the same host species. We
 focus on two species of host-specific feather lice (Phthiraptera:
 Ischnocera) that co-occur on feral rock pigeons (Columba livia). Although
 these lice are ecologically very similar, “wing lice" (Columbicola
 columbae) disperse phoretically by “hitchhiking” on pigeon flies (Diptera:
 Hippoboscidae), while "body lice" (Campanulotes compar) do not.
 Differences in the phoretic dispersal of these species are thought to
 underlie observed differences in host specificity, as well as the degree
 of host-parasite cospeciation. These ecological and macroevolutionary
 patterns suggest that body lice should exhibit more genetic
 differentiation than wing lice. We tested this prediction among lice on
 individual birds and among lice on birds from three pigeon flocks. We
 found higher levels of genetic differentiation in body lice compared to
 wing lice at two spatial scales. Our results indicate that differences in
 phoretic dispersal can explain microevolutionary differences in population
 genetic structure and are consistent with macroevolutionary differences in
 the degree of host-parasite cospeciation.
description: Data corresponding to
 Table 2aData for GLMM summary
 testing the probability that a given allele is unique to the subpopulation
 (private allele) compared to all other lice at each collection site
 respective of species.locglm.csvData corresponding to Table 2bData for GLMM summary testing the probability that a given allele is a private allele for that louse subpopulation on its individual host bird.birdglm.csvPigeon_Genotypes_bysitePigeon genotypes in genepop format.WingLice_Genotypes_bybirdWing Lice (Columbicola columbae) genotypes in genepop format.BodyLice_Genotypes_bybirdBody Lice (Campanulotes compar) genotypes in genepop format.
DOI: 10.5061/dryad.122sv
title: Data from: Bacterial quorum sensing and metabolic incentives to cooperate

description: The opportunistic pathogen Pseudomonas aeruginosa uses a cell-cell
 communication system termed “quorum sensing” to control production of
 public goods, extracellular products that can be used by any community
 member. Not all individuals respond to quorum-sensing signals and
 synthesize public goods. Such social cheaters enjoy the benefits of the
 products secreted by cooperators. There are some P. aeruginosa cellular
 enzymes controlled by quorum sensing, and we show that quorum
 sensing–controlled expression of such private goods can put a metabolic
 constraint on social cheating and prevent a tragedy of the commons.
 Metabolic constraint of social cheating provides an explanation for
 private-goods regulation by a cooperative system and has general
 implications for population biology, infection control, and stabilization
 of quorum-sensing circuits in synthetic biology.
description: Dandekar_Biolog_dataBiolog Phenotype Microarray data
DOI: 10.6084/m9.figshare.31154390
title: CO<sub>2</sub> Broadening coefficients of sulphur dioxide in the 1065–1230 cm<sup>−1</sup> spectral region

description: High-resolution spectra of SO<sub>2</sub> with high signal/noise ratio were recorded with a Bruker IFS-125HR spectrometer covering transitions from 1065 to 1230 cm<sup>−1</sup> at the spectral resolution of 0.002–0.0035 cm<sup>−1</sup>. The multispectrum fitting procedure has been applied to recover the spectral line parameters from measurements using quadratic speed-dependent Voigt (qSDV) profiles which made it possible to describe the experimental profile at the noise level. The SO<sub>2</sub> line broadening coefficients for 322 lines of ν<sub>1</sub> vibrational band were obtained. The uncertainty of the broadening coefficients for the unblended SO<sub>2</sub> absorption lines was estimated to be &lt;4%. The calculations were performed using the semiclassical method modified by including a correction factor in the calculation scheme. Line broadening parameters of SO<sub>2</sub>–CO<sub>2</sub> were computed for rotational quantum numbers <i>J</i> from 5 to 50.
DOI: 10.6084/m9.figshare.31154390.v1
title: CO<sub>2</sub> Broadening coefficients of sulphur dioxide in the 1065–1230 cm<sup>−1</sup> spectral region

description: High-resolution spectra of SO<sub>2</sub> with high signal/noise ratio were recorded with a Bruker IFS-125HR spectrometer covering transitions from 1065 to 1230 cm<sup>−1</sup> at the spectral resolution of 0.002–0.0035 cm<sup>−1</sup>. The multispectrum fitting procedure has been applied to recover the spectral line parameters from measurements using quadratic speed-dependent Voigt (qSDV) profiles which made it possible to describe the experimental profile at the noise level. The SO<sub>2</sub> line broadening coefficients for 322 lines of ν<sub>1</sub> vibrational band were obtained. The uncertainty of the broadening coefficients for the unblended SO<sub>2</sub> absorption lines was estimated to be &lt;4%. The calculations were performed using the semiclassical method modified by including a correction factor in the calculation scheme. Line broadening parameters of SO<sub>2</sub>–CO<sub>2</sub> were computed for rotational quantum numbers <i>J</i> from 5 to 50.
DOI: 10.5061/dryad.hv1kv
title: Data from: How to use (and not to use) movement-based indices for quantifying foraging behavior

description: 1. Movement based indices such as Moves Per Minute (MPM) and Proportion
 Time Moving (PTM) are common methodologies to quantify foraging behavior.
 We explore fundamental drawbacks of these indices, question the ways
 scientists have been using them, and propose new solutions. 2. To do so,
 we combined analytical and simulation models with lizards foraging data at
 the individual and species levels. 3. We found that the maximal value of
 MPM is constrained by the minimal durations of moves and stops. As a
 result, foragers that rarely move and those that rarely stop are bounded
 to similar low MPM values. This implies that (a) MPM has very little
 meaning when used alone, (b) MPM and PTM are interdependent, and (c)
 certain areas in the MPM-PTM plane cannot be occupied. We also found that
 MPM suffers from inaccuracy and imprecision. 4. We introduced a new bias
 correction formula for already published MPM data, and a novel index of
 Changes Per Minute (CPM) that uses the frequency of changes between move
 and stop bouts. CPM is very similar to MPM, but does not suffer from bias.
 Finally, we suggested a new foraging plane of Average Move and Average
 Stop durations. We hope that our guidelines of how to use (and not to use)
 movement- based indices will add rigor to the study of animals'
 foraging behavior.
description: Lizards' foraging
 behavior indicesThese file contain
 already published lizards' foraging behavior indices (MPM and PTM)
 and additional information about the duration of the original observation
 as reported by the authors. We corrected the MPM values to reduce the
 inherent bias and report how the new calculated MPM' values deviate
 from the reported ones.Halperin_etal_appendix_4.xlsx
DOI: 10.15468/dl.mx4kzz
title: Occurrence Download

description: A dataset containing 1193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.18.13_1",
 "OccurrenceStatus is Present",
 "Year 2000-2024"
 ]
}

 The dataset includes 1193 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001021-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kq685
title: Data from: Conservation genetics of the scalloped hammerhead shark in the Pacific coast of Colombia

description: Previous investigations of the population genetics of the scalloped
 hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have
 lacked information about nursery areas. Such areas are key to promoting
 conservation initiatives that can protect young sharks from threats such
 as overfishing. Here, we investigated the genetic diversity,
 phylogeography, and connectivity of S. lewini found in 3 areas of
 Colombia’s Pacific coast: around Malpelo Island and in 2 National Natural
 Parks on the Colombian Pacific mainland (Sanquianga and Ensenada de
 Utría). We analyzed mtDNA control region (CR) sequences and genotyped 15
 microsatellite loci in 137 samples of adults and juveniles. The mtDNA
 analyses showed haplotypes shared between the Colombian Pacific
 individuals sampled in this investigation and other areas in the Eastern
 Tropical Pacific, the Indo-Pacific, and with sequences previously reported
 in Colombia (Buenaventura Port), as well as 4 unique haplotypes.
 Population assignment and paternity analyses detected 3 parent–offspring
 pairs between Malpelo and Sanquianga and 1 between Malpelo and Utría.
 These results indicate high genetic connectivity between Malpelo Island
 and the Colombian Pacific coast, suggesting that these 2 areas are
 nurseries for S. lewini. This is, to our knowledge, the first evidence of
 nursery areas identified for the scalloped hammerhead shark anywhere in
 the world. Additional conservation planning may be required to protect
 these nursery habitats of this endangered shark species.
description: SphyrnaGenotypesdryadThis file contains all genotypes obtained from scalloped hammerhead sharks from the Pacific of Colombia, around Malpelo Island and in two costal protected areas, Utría and Sanquianga
DOI: 10.5061/dryad.th198
title: Data from: Positive relationships between association strength and phenotypic similarity characterize the assembly of mixed-species bird flocks worldwide

description: Competition theory predicts that communities at small spatial scales
 should consist of species more dissimilar than expected by chance. We find
 a strikingly different pattern in a multi-continent dataset (55
 presence-absence matrices from 24 locations) on the composition of
 mixed-species bird flocks, important subunits of local bird communities
 the world over. Using null models and randomization tests followed by
 meta-analysis, we find the association strength of species in flocks to be
 strongly related to similarity in body size and foraging behavior, and
 higher for congeneric compared with non-congeneric species pairs. Given
 the small spatial scale of our individual analyses, differences in habitat
 preferences of species are unlikely to have caused these association
 patterns; therefore, the patterns are most likely the outcome of species
 interactions. Extending group-living and social information use theory to
 a heterospecific context, we discuss potential behavioral mechanisms
 leading to positive interactions among similar species in flocks as well
 as ways in which competition costs are reduced. Our findings highlight the
 need to consider positive interactions along with competition when seeking
 to explain community assembly.
description: datafiles_Sridhar_et_al_2012
DOI: 10.5061/dryad.v5g6r80
title: Data from: Complex interactions between local adaptation, phenotypic plasticity, and sex affect vulnerability to warming in a widespread marine copepod

description: Predicting the response of populations to climate change requires
 knowledge of thermal performance. Genetic differentiation and phenotypic
 plasticity affect thermal performance, but the effects of sex and
 developmental temperatures often go uncharacterized. We used common garden
 experiments to test for effects of local adaptation (Florida versus
 Connecticut temperatures), developmental phenotypic plasticity (18oC vs.
 22oC), and individual sex on thermal performance of the ubiquitous
 copepod, Acartia tonsa. Females had higher thermal tolerance than males in
 both populations, while the Florida population had higher thermal
 tolerance compared to the Connecticut population. An effect of
 developmental phenotypic plasticity on thermal tolerance was observed only
 in the Connecticut population. Ignoring sex-specific differences may
 result in a severe underestimation of population-level impacts of warming
 (i.e. - population decline due to sperm limitation). Further, despite
 having a higher thermal tolerance, Southern populations may be more
 vulnerable to warming as they lack the ability to respond to increases in
 temperature through phenotypic plasticity.
description: Thermal Survivorship
 DataResults from individual
 survivorship assays after 24-hour acute heat stress. Columns correspond to
 Population of origin, Developmental temperature, Stress temperature,
 Individual's sex, and Survivorship (0 = mortality, 1 =
 survival).tpc_data.xlsxAcartia tonsa Body Size MeasurementsProsome length measurements for mature male and female Acartia tonsa individuals from Florida and Connecticut populations. Measurements were made using Image-J.body_size_data.xlsx
DOI: 10.5061/dryad.7h4r3
title: Data from: What doesn’t kill you might make you stronger: functional basis for variation in body armour

description: 1. Predation has been proposed to be a selective agent in the evolution of
 morphological antipredator strategies in prey. Among vertebrates, one of
 the morphological traits that evolved multiple times is body armour,
 including carapaces, thickened keratinized scales and plates of dermal
 bone. 2. It has been generally assumed that body armour provides
 protection against a predatory attack; yet, few explicit tests of the
 hypothesis exist. Cordylidae, a relatively small family of southern
 African lizards, show considerable variation in the degree of body armour.
 Hence, this family provides an opportunity to test the hypothesis that
 body armour serves as protection against predators. 3. Experiments were
 conducted to test whether the bite forces of four species of mammalian
 predators were high enough to penetrate the skins of Karusasaurus
 polyzonus, Namazonurus peersi, Cordylus cordylus and Cordylus macropholis,
 as well as those of Ouroborus cataphractus individuals originating from
 three localities that differed in their predator diversity. Furthermore,
 histological techniques were used to test whether variation in skin
 toughness was associated with concomitant changes in the degree of
 epidermal (i.e. β-keratin) and dermal (i.e. osteoderm) armour. 4. The skin
 toughness values for four out of five cordylid lizards tested in this
 study were well below the bite forces of the mammalian predators. In
 contrast, the thick osteoderms in the dermis of O. cataphractus can
 withstand bites from several mongoose species. However, the significant
 variation in body armour that is present between the three populations of
 O. cataphractus does not seem to be related to predator diversity. 5. It
 is concluded that body armour can serve as protection against predation in
 O. cataphractus, but that alternative selection pressures, such as
 thermoregulation or predation by snakes, presumably underlie variation in
 defensive morphology in the other cordylid lizards.
description: Skin
 ToughnessSkin toughness values
 (in N) for five species of cordylid lizards using the skulls of four
 species of (mongoose) predatorsDryad1_Skin
 Toughness.xlsxSkin
 MorphologyThickness of the
 osteoderm and beta-keratin layer (in mm) of dermal skin
 sectionDryad2_Skin
 Morphology.xlsxMongoose Bite
 ForcetTeoretical estimates of
 bite force (in N) for four mongoose speciesDryad3_Mongoose Bite
 Force.xlsx