cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9b245g0
title: Data from: A human impact metric for coastal ecosystems with application to seagrass beds in Atlantic Canada

description: Coastal biogenic habitats are vulnerable to human impacts from both
 terrestrial and marine realms. Yet the broad spatial scale used in current
 approaches of quantifying anthropogenic stressors is not relevant to the
 finer scales affecting most coastal habitats. We developed a standardized
 human impact metric that includes five bay-scale and four local-scale (0–1
 km) terrestrial and marine-based impacts to quantify the magnitude of
 anthropogenic impacts to coastal bays and nearshore biogenic habitats. We
 applied this metric to 180 seagrass beds (Zostera marina), an important
 biogenic habitat prioritized for marine protection, in 52 bays across
 Atlantic Canada. The results show that seagrass beds and coastal bays
 exist across a wide human impact gradient and provide insight into which
 are the most and least affected by human threats. Generally, land
 alteration, nutrient loading, and shellfish aquaculture were higher in the
 Gulf of St. Lawrence, whereas invasive species and fishing activities were
 higher along the Atlantic coast. Sixty-four percent of bays were at risk
 of seagrass decline from nitrogen loading. We also found high within-bay
 variation in impact intensity, emphasizing the necessity of quantifying
 impacts at multiple spatial scales. We discuss implications for management
 and conservation planning, and application to other coastal habitats in
 Canada and beyond.
description: Murphy et al. 2019
 FACETS supplementary material 2Bay scale impact scores
 for Murphy et al. 2019 FACETSMurphyetal_2019_FACETS_supplementary_material2_May2019.csvMurphyetal_2019_FACETS_supplementary_material3_May2019Local scale impact metrics for Murphy et al. 2019 FACETS
DOI: 10.5061/dryad.1jv12nj
title: Data from: Testing for local adaptation in adult male and female fitness among populations evolved under different mate competition regimes

description: Mating/fertilization success and fecundity are influenced by sexual
 interactions among individuals, the nature and frequency of which can vary
 among different environments. The extent of local adaptation for such
 adult fitness components is poorly understood. We allowed 63 populations
 of Drosophila melanogaster to independently evolve in one of three mating
 environments that alter sexual interactions: one involved enforced
 monogamy while the other two permitted polygamy in either structurally
 simple standard fly vials or in larger ‘cages’ with added complexity.
 Adult male and female reproductive fitness were measured after 16 and 28
 generations respectively via full reciprocal transplants. In males,
 reciprocal local adaptation was observed between the monogamy and simple
 polygamy treatments, consistent with the evolution of reproductively
 competitive males under polygamy that perform poorly under monogamy
 because they harm their only mate. However, males evolved in the complex
 polygamy treatment performed similarly or better than all other males in
 all mating environments, consistent with previous results showing higher
 genetic quality in this treatment. Differences in female fitness were more
 muted, suggesting selection on females was less divergent across the
 mating treatments and echoing a common pattern of greater phenotypic and
 expression divergence in males than females.
description: MaleAdultFitnessData_DryadData from 'male reproductive fitness assay' - a reciprocal transplant in which males from all 21 experimental populations from within a given larval adaptation set, and the ancestor, were all assayed in each of the three mating environments (i.e. the mating environment in which they had been evolving as well as the other two mating environments). Rows are individual (ancestral) females and 'DsRed_offspring' and 'wildtype_offspring' denote the number of offspring of the given phenotype produced by this female. Mating treatments and mating environments are as described in the publication.FemaleAdultFitnessData_DryadData from the 'Female Reproductive Fitness Assay' - a reciprocal transplant in which females from all 21 populations (i.e. seven from each of the three evolutionary mating treatments) and the ancestral population were all assayed in each of the three assay mating environments. In all cases males in these assays came from the ancestral population. 'No.egg' indicates the total number of eggs produced by a single female in a given assay. 'Average fecundity' is the average of all females in a given replicate. Mating treatments and assay environments are as described in the publication.MatingRateData_DryadData from the preliminary Assay on the 'Effect of mating environment on mating rate', as described in the Supplemental materials of the publication. The assay was performed over three days (1-3) with hourly observations (time; 24h clock) in which the number of observed matings was recorded ('Number_of_matings').
DOI: 10.5061/dryad.rh4172f
title: Data from: Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them

description: Despite the ubiquitous use of statistical models for phylogenomic and
 population genomic inferences, this model-based rigor is rarely applied to
 post-hoc comparison of trees. In a recent study, Garba and colleagues
 derived new methods for measuring the distance between two gene trees
 computed as the difference in their site pattern probability
 distributions. Unlike traditional metrics that compare trees solely in
 terms of geometry, these measures consider gene trees and associated
 parameters as probabilistic models that can be compared using standard
 information theoretic approaches. Consequently, probabilistic measures of
 phylogenetic tree distance can be far more informative than simply
 comparisons of topology and/or branch lengths alone. However, in their
 current form, these distance measures are not suitable for the comparison
 of species tree models in the presence of gene tree heterogeneity. Here we
 demonstrate an approach for how the theory of Garba et al. (2018), which
 is based on gene tree distances, can be extended naturally to the
 comparison of species tree models. Multispecies coalescent models (MSC)
 parameterize the discrete probability distribution of gene trees
 conditioned upon a species tree with a particular topology and set of
 divergence times (in coalescent units), and thus provide a framework for
 measuring distances between species tree models in terms of their
 corresponding gene tree topology probabilities. We describe the
 computation of probabilistic species tree distances in the context of
 standard MSC models, which assume complete genetic isolation
 post-speciation, as well as recent theoretical extensions to the MSC in
 the form of network-based MSC models that relax this assumption and permit
 hybridization among taxa. We demonstrate these metrics using simulations
 and empirical species tree estimates and discuss both the benefits and
 limitations of these approaches. We make our species-tree distance
 approach available as an R package called pSTDistanceR, for open use by
 the community.
description: _SupplementaryText_29April2019aSupplementary TextSupplementaryFigure01_11Dec2018Supplementary Figure 1
DOI: 10.5061/dryad.pr996gj
title: Data from: Cross-sex genetic covariances limit the evolvability of wing-shape within and among species of Drosophila

description: The independent evolution of males and females is potentially constrained
 by both sexes inheriting the same alleles from their parents. This genetic
 constraint can limit the evolvability of complex traits; however, there
 are few studies of multivariate evolution that incorporate cross-sex
 genetic covariances in their predictions. Drosophila wing-shape has
 emerged as a model high-dimensional phenotype; wing-shape is highly
 evolvable in contemporary populations, and yet perplexingly stable across
 phylogenetic timescales. Here we show that cross-sex covariances in D.
 melanogaster, given by the B-matrix, may considerably bias wing-shape
 evolution. Using random skewers, we show that B would constrain the
 response to antagonistic selection by 90%, but would double the response
 to concordant selection. Both cross-sex within-trait and cross-sex
 cross-trait covariances determined the response to antagonistic selection,
 but only cross-sex within-trait covariances facilitated the response to
 concordant selection. Similar patterns were observed when selection was
 applied in the direction of extant sexual dimorphism in D. melanogaster,
 and in directions of most and least dimorphic variation across the
 Drosophila phylogeny. Our results highlight the importance of considering
 between-sex genetic covariances when making predictions about evolution on
 both macro- and micro- evolutionary timescales, and may provide one more
 explanatory piece in the puzzle of stasis.
description: melanogaster_data
 dryadwabassoPCsspecies data dryad
DOI: 10.5061/dryad.3h75c0h
title: Data from: Marital stability in a pastoralist society

description: We examined how individual investment was associated with the duration of
 marriage partnerships in a pastoralist society of Amdo Tibetans in China.
 We collected demographic and socioeconomic data from 420 women and 369 men
 over 5 villages to assess which factors predicted partnership length. We
 found that the payment of dowry and bridewealth from both sides of the
 family predicted marriage stability. The production of offspring,
 regardless of their survivorship, also had a positive effect on marriage
 duration, as did trial marriage, a time period before formal marriage.
 Finally, we found that If both bride and groom invest resources initially
 into a partnership—whether wealth or labour—their subsequent partnership
 is stronger than couples who do not make such investments. This paper adds
 to our understanding of complex social institutions like marriage from a
 behavioural ecological perspective.
description: brideprice
DOI: 10.5061/dryad.7nq1c6s
title: Data from: Long-lasting vocal plasticity in adult marmoset monkeys

description: Humans exhibit a high level of vocal plasticity in speech production which
 allows us to acquire both native and foreign languages, dialects and adapt
 to local accents in social communication. In comparison, non-human
 primates exhibit limited vocal plasticity, especially in adulthood, which
 would limit their ability to adapt to different social and environmental
 contexts in vocal communication. Here we quantitatively examined the
 ability of adult common marmosets (Callithrix jacchus), a highly vocal New
 World primate species, to modulate their vocal production in social
 contexts. While recent studies have demonstrated vocal learning in
 developing marmosets, we know much less on the extent of vocal learning
 and plasticity in adult marmosets. We found in the present study that
 marmosets were able to adaptively modify the spectrotemporal structure of
 their vocalizations when they encountered interfering sounds. Our
 experiments showed that marmosets shifted the spectrum of their
 vocalizations away from the spectrum of the interfering sounds in order to
 avoid the overlap. More interestingly, we found that marmosets made
 predictive and long-lasting spectral shifts in their vocalizations after
 they had experienced a particular type of interfering sounds. These
 observations provided evidence for directional control of the vocalization
 spectrum and long-term vocal plasticity by adult marmosets. Findings
 reported here have important implications for the ability of this New
 World primate species in voluntarily and adaptively controlling their
 vocal production in social communication.
description: Marmoset vocalization
 dataJammingAllData.mat
 contains a MATLAB structure array “SbjData” which stores the experimental
 data for the four subjects. Each row in “SbjData” is a subject. The first
 column is for low-frequency noise perturbation (and the baseline preceding
 it) whereas the second column is for high-frequency noise perturbation
 (and the baseline preceding it). “SbjData.Param” stores various parameters
 used in the analysis and the experiment info. For example, “exp_day”
 contains the day number for each experimental session. Perturbation
 sessions are labeled as “Jamming” in the data structures.
 “SbjData.Measure.FreqPrePostWin” stores the actual data, as described
 below for its several fields. “Jamming” and “Baseline” contains the
 original recorded data for the perturbation and baseline sessions,
 respectively. “JammingDT” and “BaselineDT” are the detrended data. Inside
 these matrices, Column 1 labels separate sessions; Column 2 is the call
 onset time (sec); Column 4 is the fundamental frequency of the call (Hz,
 original or detrended); Column 6: 0 for baseline; 1 for not-perturbed, 2
 for perturbed calls. “FittedTimeCourse{2}” is the fundamental frequency
 profile of baseline sessions [Time (s), Freq (Hz)].
 “FittedTimeCourse_Jamming{2}” is the fundamental frequency profile of
 perturbation sessions.JammingAllData.mat
DOI: 10.5061/dryad.5352kv8
title: Data from: Bearding the scorpion in his den: desert isopods take risks to validate their ‘landscape of fear’ assessment

description: Animals balance the risk of predation against other vital needs by
 adjusting their spatial behavior to match spatiotemporal variation in
 predation risk. To map this ‘landscape of fear’, prey use evolutionary
 rules of thumbs that are associated with the activity and hunting
 efficiency of predators. In addition, prey acquire perceptual information
 about the presence, identity, and state of potential predators and use
 these cues to focus their acute anti-predatory responses. Our goal was to
 explore if and how prey also use such perceptual information that decays
 with time to update their spatiotemporal risk assessment. We placed
 scorpions in freshly dug burrows and recorded the isopods’ spatial
 activity and their defense behavior upon encountering the burrows straight
 after settling the scorpions and seven days later. To corroborate our
 understanding, we also examined the isopods’ detailed reactions towards
 deserted scorpion burrows. The isopods reacted defensively to scorpion
 burrows during their first encounter. After seven days, proportionally
 more isopods approached the scorpion burrows on their way out for foraging
 and fewer isopods encountered it on their way back. No changes in the
 spatial activity were observed towards deserted burrows. In addition, on
 the eighth day, more isopods entered the risky area near the scorpion
 burrows when leaving their own burrow than on the first encounter. The
 results suggest that isopods used predator cues to readjust the ‘landscape
 of fear’. Yet, rather than avoiding the dangerous areas altogether, the
 isopods implemented risky inspection behavior, validating whether the
 danger is actual. Our findings imply that inspection behavior toward
 predators can be used for future planning of prey spatial activity,
 offsetting possible ‘information decay costs’.
description: DataAll behavioral data
 collected throughout the experiment
DOI: 10.5061/dryad.54h0t79
title: Data from: Symposium article: Which line to follow? the utility of different line-fitting methods to capture the mechanism of morphological scaling

description: Bivariate morphological scaling relationships describe how the sizes of
 two traits co-vary among adults in a population. In as much as body shape
 is reflected by the relative size of various traits within the body,
 morphological scaling relationships capture how body shape varies with
 size, and therefore have been used widely as descriptors of morphological
 variation within and among species. Despite their extensive use, there is
 continuing discussion over which line-fitting method should be used to
 describe linear morphological scaling relationships. Here I argue that the
 ‘best’ line-fitting method is the one that most accurately captures the
 proximate developmental mechanisms that generate scaling relationships.
 Using mathematical modeling, I show that the ‘best’ line-fitting method
 depends on the pattern of variation among individuals in the developmental
 mechanisms that regulate trait size. For Drosophila traits, this pattern
 of variation indicates that major axis regression is the best line-fitting
 method. For morphological traits in other animals, however, other
 line-fitting methods may be more accurate. I provide a simple web-based
 application for researchers to explore how different line-fitting methods
 perform on their own morphological data.
description: Analysis of Dreyer and
 Shingleton Table 1: RmdThe R markdown document
 detailing the analysis used to generate the data in Table 1 of Shingleton
 2019.Analysis of Dreyer and
 Shingleton Data .RmdAnalysis of Dreyer and
 Shingleton Table 1: PDFA PDF detailing the
 analysis used to generate the data in Table 1 of Shingleton
 2019.Analysis_of_Dreyer_and_Shingleton_Data_.pdfDreyer_and_Shingleton_dataData used in the analysis for Table 1 in Shingleton 2019. Data are the size of the thorax, wing, palp, anal plate, femur of the first leg, and genital arch for 50 males from 40 isogenic lineages.Analysis of Bakota and Others: RmdThe R markdown document detailing the analysis used to generate the data in Table 3 and Table S1 of Shingleton 2019.Analysis of Bakota and Others.RmdAnalysis_of_Bakota_and_Others: PDFA PDF detailing the analysis used to generate the data in Table 3 and Table S1 of Shingleton 2019.Analysis_of_Bakota_and_Others.pdfBakota_et_al_dataData used in the analysis for Table 3 and Table S1 in Shingleton 2019. Data are the size of the pupa and wing for flies from 87 isogenic lineages.ui.Rui.R object for Shiny Appserver.Rserver.R function for Shiny AppRun Me ScriptR script to run Shiny App. Place 'Run Me' script, ui.R and server.R files in the same folder, edit the 'Run Me' script to make the folder the working directory, and run the 'Run Me' script.Run Me.R
DOI: 10.5061/dryad.c7g30cp
title: Data from: Resource constraints highlight complex microbial interactions during lake biofilm development

description: Abstract 1. This study evaluated how the availability of nutrients and
 organic carbon interact to influence the associations between autotrophic
 and heterotrophic microorganisms during lake biofilm development.
 Considering that decomposers are often better competitors for nutrients
 than producers in aquatic environments, we hypothesized that heterotrophs
 would outcompete autotrophs for available nutrients unless heterotrophs
 were limited by organic carbon provided by autotrophs. 2. To test our
 hypothesis, we evaluated autotrophic (algae) and heterotrophic (fungi,
 bacteria) biomass in response to a factorial enrichment of nutrients
 (nitrogen and phosphorus in combination) and glucose using nutrient
 diffusing substrates with either inorganic or organic discs in a subalpine
 lake. In the field, nutrient diffusing substrates were exposed to either
 natural sunlight or placed under a darkened experimental canopy to
 evaluate the response of heterotrophs to nutrients and carbon subsidies in
 the presence or absence of algae. We expected that heterotrophs would be
 limited by organic carbon on inorganic substrates in the absence of
 autotrophic production (i.e., dark treatments), and that organic
 substrates would provide a carbon subsidy for heterotrophic metabolism. 3.
 Fungi were stimulated by nutrient enrichment on inorganic substrates in
 the presence of algae (light treatment), but not in the dark (without
 algae). The response of fungi to algal presence on inorganic substrates
 was similar in magnitude to the response of fungi to nutrients and glucose
 substrates incubated in the dark. In contrast to our expectations,
 elevated algal biomass did not stimulate heterotrophic bacteria in the
 presence of elevated nutrient levels on inorganic substrates, possibly
 owing to antagonistic interactions between bacteria and fungi. 4. The
 positive effect of nutrients on algal biomass was significantly reduced in
 favor of heterotrophs when nutrients were combined with glucose,
 suggesting that heterotrophs were able to outcompete algae for available
 nutrients in the absence of carbon limitation. 5. Synthesis. These results
 expand our understanding of how the availability of limiting resources
 govern the outcomes of complex interactions among microorganisms in
 aquatic biofilms, and suggest that background levels of organic carbon
 regulate producer and decomposer responses to nutrient availability during
 biofilm development.
description: Wyatt et
 al_2019_datasetThese data were
 collected as part of a biofilm experiment conducted in Castle Lake,
 California. The data file is in csv format.
DOI: 10.5061/dryad.nf94810
title: Data from: Visual modelling supports the potential for prey detection by means of diurnal active photolocation in a small cryptobenthic fish

description: Active sensing has been well documented in animals that use echolocation
 and electrolocation. Active photolocation, or active sensing using light,
 has received much less attention, and only in bioluminescent nocturnal
 species. However, evidence has suggested the diurnal triplefin
 Tripterygion delaisi uses controlled iris radiance, termed ocular sparks,
 for prey detection. While this form of diurnal active photolocation was
 behaviourally described, a study exploring the physical process would
 provide compelling support for this mechanism. In this paper, we
 investigate the conditions under which diurnal active photolocation could
 assist T. delaisi in detecting potential prey. In the field, we sampled
 gammarids (genus Cheirocratus) and characterized the spectral properties
 of their eyes, which possess strong directional reflectors. In the
 laboratory, we quantified ocular sparks size and their angle-dependent
 radiance. Combined with environmental light measurements and known
 properties of the visual system of T. delaisi, we modeled diurnal active
 photolocation under various scenarios. Our results corroborate that
 diurnal active photolocation should help T. delaisi detect gammarids at
 distances relevant to foraging, 4.5 cm under favourable conditions and up
 to 2.5 cm under average conditions. To determine the prevalence of diurnal
 active photolocation for micro-prey, we encourage further theoretical and
 empirical work.
description: Average gammarid body
 reflectanceSpectrophotometric data
 for body reflectance of Cheirocratus gammaridsAverage gammarid body
 transmissionSpectrophotometric
 transmission measurements of Cheirocratus gammarid bodyBackground reflectance
 Haliopteris filicianaSpectrophotometric
 measurements of Haliopteris filicianaCoaxial reflectance
 values categoricalReflective properties of
 Gammarid eyes measured with coaxial light sourceDownwelling and
 sidewelling illuminant for analysesDownwelling and
 sidewelling light fieldsEye reflectance
 conversion values categoricalConversion factors to
 produce non-coaxial reflectance values from co-axial reflectance values
 for gammarid eyesOcular media
 valuesTransmission properties
 of the ocular media of Tripterigyon delaisiOcular spark conversion
 on continuous scaleConversion curves for
 transforming downwelling irradiance into ocular spark
 radianceSA scores Gammarid as
 perceived by Td pupilSolid angle of the
 gammarid eye as perceived from the pupil of T. delaisi based on the
 interaction distanceSA scores Os as
 perceived by Gammarid eye MATRIXSolid angles of the
 Ocular spark from T delaisi as perceived by the gammarid eye based on the
 interaction distance