cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.66ft5
title: Data from: Can the Fisher-Lande process account for birds of paradise and other sexual radiations?

description: Models of the Fisher‐Lande process (FLP) have been used successfully to
 explore many aspects of evolution by sexual selection. Despite this
 success, quantitative tests of these models using data from sexual
 radiations are rare. Consequently, we do not know whether realistic
 versions of the FLP can account for the extent and the rate of evolution
 of sexually selected traits. To answer this question, we generalize the
 basic FLP model of sexual coevolution and compare predictions of that
 basic model with patterns observed in an iconic sexual radiation, birds of
 paradise. Our model tracks the coevolution of male and female traits (two
 in each sex) while relaxing some restrictive assumptions. Using computer
 simulations, we evaluate the behavior of the model and confirm that it is
 an Ornstein‐Uhlenbeck (OU) process. We also assess the ability of the FLP
 to account for the quantitative aspects of ornament evolution in the genus
 Paradisaea using published measurements of display traits and a phylogeny
 of the genus. Finally, we use the program OUwie to compare model fits to
 generic OU and Brownian motion processes and to estimate FLP parameters.
 We show that to explain the sexual radiation of the genus Paradisaea one
 must either invoke extremely weak stabilizing selection on female mating
 preferences or allow the preference optimum to undergo Brownian motion at
 a modest rate.
description: male_wing4Male wing length data in OUwie formattopo7OUwie tree fileLeCroy dataMeasurements of wing, tail, and tarsus lengths in 14 populations of birds of paradise in the genus Paradisaea (from LeCroy, M. 1981. The genus Paradisaea - display and evolution. American Museum Novitates 2714:1-52.). Measurements for each population (mm) are standardized (divided by average within population standard deviation for that trait and sex*).R script for fig 4DThis R program runs a stochastic simulation of the FLP in 100 populations for 500 generations and then plots results at generation 500 (fig. 4D). See Appendix A for the equations used in this program. See Table 2 for parameter values used in this and other figures.
DOI: 10.5061/dryad.949nc
title: Data from: A new framework for analysing automated acoustic species detection data: occupancy estimation and optimization of recordings post-processing

description: The development and use of automated species detection technologies, such
 as acoustic recorders, for monitoring wildlife are rapidly expanding.
 Automated classification algorithms provide cost- and time-effective means
 to process information-rich data, but often at the cost of additional
 detection errors. Appropriate methods are necessary to analyse such data
 while dealing with the different types of detection errors. We developed a
 hierarchical modelling framework for estimating species occupancy from
 automated species detection data. We explore design and optimization of
 data post-processing procedures to account for detection errors and
 generate accurate estimates. Our proposed method accounts for both
 imperfect detection and false-positive errors and utilizes information
 about both occurrence and abundance of detections to improve estimation.
 Using simulations, we show that our method provides much more accurate
 estimates than models ignoring the abundance of detections. The same
 findings are reached when we apply the methods to two real datasets on
 North American frogs surveyed with acoustic recorders. When false
 positives occur, estimator accuracy can be improved when a subset of
 detections produced by the classification algorithm is post-validated by a
 human observer. We use simulations to investigate the relationship between
 accuracy and effort spent on post-validation, and found that very accurate
 occupancy estimates can be obtained with as little as 1% of data being
 validated. Automated monitoring of wildlife provides opportunity and
 challenges. Our methods for analysing automated species detection data
 help to meet key challenges unique to these data and will prove useful for
 many wildlife monitoring programmes.
description: Data S1 - Pig Frog
 DatasetThese are the detection
 data, used in the Pig frog analysis, including (1) all types of
 detections, (2) true positive detections and (3) false positive
 detections.Data S1 - Pig
 Frog.txtData S2 - Green
 TreefrogThese are the detection
 data, used in the Green treefrog analysis, including (1) all types of
 detections, (2) true positive detections and (3) false positive
 detections.Acoustic Detection
 Simulation CodeR code used to simulate
 acoustic detection data. The detection process includes a rate of false
 positive detections occurrence.Appendix-S2 -- code for
 simulation -- 10-15-2018.txtModel
 codeCode, in BUGS language,
 to implement the three models presented in the paper.Appendix-S1 -- model
 code.txt
DOI: 10.34740/kaggle/dsv/14641437
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.cg4qp
title: Data from: Conserved class of queen pheromones stops social insect workers from reproducing

description: A major evolutionary transition to eusociality with reproductive division
 of labor between queens and workers has arisen independently at least 10
 times in the ants, bees, and wasps. Pheromones produced by queens are
 thought to play a key role in regulating this complex social system, but
 their evolutionary history remains unknown. Here, we identify the first
 sterility-inducing queen pheromones in a wasp, bumblebee, and desert ant
 and synthesize existing data on compounds that characterize female
 fecundity in 64 species of social insects. Our results show that queen
 pheromones are strikingly conserved across at least three independent
 origins of eusociality, with wasps, ants, and some bees all appearing to
 use nonvolatile, saturated hydrocarbons to advertise fecundity and/or
 suppress worker reproduction. These results suggest that queen pheromones
 evolved from conserved signals of solitary ancestors.
description: Bioassay and comparative
 analysis dataB terrestris
 bioassays.txt: Bombus terrestris bioassay data; Cataglyphis iberica
 bioassays.txt: Cataglyphis iberica bioassay data; V vulgaris
 bioassays.txt: Vespula vulgaris bioassay data; character states.csv:
 character matrix used in the comparative analysis; phylogeny.nex:
 phylogeny used for the comparative analysis (in Nexus/Mesquite
 format)data.zip
DOI: 10.5061/dryad.57vg809
title: Data from: Extended phenotypes and foraging restrictions: ant nest entrances and resource ingress in leaf-cutting ants

description: Several factors may restrict the acquisition of food to below the levels
 predicted by the optimization theory. However, how the design of
 structures that animals build for foraging restrict the entry of food are
 less known. Using scaling relationships we determined whether the design
 of the entrances of leaf-cutting ant nests restricts resource input into
 the colony. We measured nests and foraging parameters in 25 nests of Atta
 cephalotes in a tropical rain forest. Ant flux was reduced to up to 60% at
 nest entrances. The width of all entrances per nest increased at similar
 rates as nest size, but the width of nest entrances increased with the
 width of its associated trail at rates below those expected by isometry.
 The fact that entrance widths grow slower than trail widths suggests that
 the enlargement of entrance holes does not reach the dimensions needed to
 avoid delays when foraging rates are high and loads are big. The
 enlargement of nest entrances appears to be restricted by the digging
 effort required to enlarge nest tunnels, and by increments in the risk of
 inundation, predator/parasitoid attacks, and microclimate imbalances
 inside the nest. The design of the extended phenotypes can also restrict
 the ingress of food into the organisms, offering additional evidence to
 better understand eventual controversies between empirical data and the
 foraging theory.
description: Data base
 ms-repositoryData file that includes
 ant nest dimensions, nest entrances dimensions, ant speed, ant
 flux
DOI: 10.5061/dryad.ts57v
title: Data from: Breeding bird species diversity across gradients of land use from forest to agriculture in Europe

description: Loss, fragmentation and decreasing quality of habitats have been proposed
 as major threats to biodiversity world-wide, but relatively little is
 known about biodiversity responses to multiple pressures, particularly at
 very large spatial scales. We evaluated the relative contributions of four
 landscape variables (habitat cover, diversity, fragmentation and
 productivity) in determining different components of avian diversity
 across Europe. We sampled breeding birds in multiple 1-km2 landscapes,
 from high forest cover to intensive agricultural land, in eight countries
 during 2001−02. We predicted that the total diversity would peak at
 intermediate levels of forest cover and fragmentation, and respond
 positively to increasing habitat diversity and productivity; forest and
 open-habitat specialists would show threshold conditions along gradients
 of forest cover and fragmentation, and respond positively to increasing
 habitat diversity and productivity; resident species would be more
 strongly impacted by forest cover and fragmentation than migratory
 species; and generalists and urban species would show weak responses.
 Measures of total diversity did not peak at intermediate levels of forest
 cover or fragmentation. Rarefaction-standardized species richness
 decreased marginally and linearly with increasing forest cover and
 increased non-linearly with productivity, whereas all measures increased
 linearly with increasing fragmentation and landscape diversity. Forest and
 open-habitat specialists responded approximately linearly to forest cover
 and also weakly to habitat diversity, fragmentation and productivity.
 Generalists and urban species responded weakly to the landscape variables,
 but some groups responded non-linearly to productivity and marginally to
 habitat diversity. Resident species were not consistently more sensitive
 than migratory species to any of the landscape variables. These findings
 are relevant to landscapes with relatively long histories of human
 land-use, and they highlight that habitat loss, fragmentation and
 habitat-type diversity must all be considered in land-use planning and
 landscape modeling of avian communities.
description: Bioassess bird
 dataLandscape variables and
 avian point-count species richness data collected in the BioAssess project
 2001-2002 in eight European countriesbioassess-birds-corrected.txt
DOI: 10.5061/dryad.g0870
title: Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar

description: A genotyping assay for the Ion Torrent Ion PGM platform was developed for
 fast and cost-effective targeted genotyping of key single nucleotide
 polymorphisms (SNPs) earlier identified using a genome-wide SNP array in
 Atlantic salmon Salmo salar. The method comprised a simple primer design
 step for multiplex-polymerase chain reaction (PCR), followed by two rounds
 of Ion Torrent Ion PGM sequencing to empirically evaluate marker
 efficiency in large multiplexes and to optimise or exclude them when
 necessary. Of 282 primer pairs initially tested, 217 were successfully
 amplified, indicating good amplification success (&gt;75%). These
 markers included the sdy partial gene product to determine genetic sex, as
 well as three additional modules comprising SNPs for assessing neutral
 genetic variation (NSNP = 150), examining functional genetic variation
 associated with sea age at maturity (NSNP = 5), and for performing genetic
 subpopulation assignment (NSNP = 61). The assay was primarily developed to
 monitor long-term genetic changes in S. salar from the Teno River, but
 modules are likely suitable for application in a wide range of S. salar
 populations. Furthermore, the fast and versatile assay development
 pipeline offers a strategy for developing targeted sequencing assays in
 any species.
description: Aykanat et al (2016)
 JFB, targeted genotyping by sequencingobject to call genotypes
 of targeted SNPs in the multiplex panels from raw fastq reads, and assess
 genotyping quality and unspecific product reads.Aykanat et al 2016 JFB
 codes_rev1.zip
DOI: 10.5061/dryad.mm720
title: Data from: Test flattening in the larger foraminifer Heterostegina depressa: predicting bathymetry from axial sections

description: Previous attempts to quantify the test flattening trend in Heterostegina
 depressa with water depth have been rather unsuccessful. Due to its broad
 depth distribution, H. depressa is a perfect model species to calibrate
 test flattening as a bathymetric signal for fossil assemblages. This might
 enable us to better reconstruct palaeoenvironments of fossil larger
 foraminiferal communities or even provide clues on the degree of transport
 in allochthonous deposits. In this study we used growth-independent
 functions to describe the change of test thickness throughout ontogeny.
 Four growth-invariant characters, deriving from these functions, clearly
 quantify a transition of individuals with thicker to thinner central parts
 along the water depth gradient. This is probably controlled by light
 intensity because the photosymbionts of H. depressa (diatoms) are most
 effective at low irradiation levels. Thus, shallower specimens grow
 thicker to reduce light penetration, whereas specimens living deeper than
 the light optimum increase their surface by flattening to obtain a better
 light exposure.
description: Supplementary
 Data1SupplementaryData2Supplementary Data3Template for the calculation of the growth-invariant characters
DOI: 10.5061/dryad.8mv2j
title: Data from: Natural and anthropogenic sounds reduce song performance: insights from two emberizid species

description: Anthropogenic sounds influence animal vocal behaviour, species
 distributions, and community assemblages. Natural sounds also have the
 potential to affect the behaviour and ecology of animals, but it is
 currently unknown if the effects of natural sounds match those of
 anthropogenic sounds. Here, we quantified and compared the effects of
 natural and anthropogenic sounds on avian song performance by calculating
 trade-off frontiers based on trill rate and bandwidth of 2 emberizid
 species. Chipping sparrows (Spizella passerina) and white-crowned sparrows
 (Zonotrichia luecophrys) were recorded in areas with and without
 anthropogenic sound and along a natural sounds gradient generated from
 ocean surf, respectively. We analysed individuals’ song performance
 relative to the trade-off frontier and found that both species vocalizing
 in environments with louder background sounds sang songs that were
 significantly further below the trade-off frontier than songs sung by
 birds in quiet settings. Chipping sparrows vocalizing in noisy areas sang
 almost twice as far below the trade-off frontier than individuals in quiet
 areas, and white-crowned sparrow song performance declined by ~25% with
 each 3 dB(A) increase in environmental sounds, or halving the size of a
 signaller’s listening area. These results suggest that natural and
 anthropogenic sounds can have a significant effect on song performance, a
 trait known to influence the outcome of male-male contests and influence
 female mate choices. Considering that natural sounds are pervasive, quiet
 acoustic refuges may be far more important than previously thought, and
 anthropogenic development may be infringing on larger portions of prime
 habitat than we realize.
description: Chipping sparrow song
 meansCHSP_Song_Means_DRYAD.csvCHSPREADME.csvChipping sparrow song performance scriptChipping_Sparrow_Song_Performance_Script.RWhite-crowned sparrow song meansWCSP_FINAL_Data_DRYAD.csvWCSPREADME.csvWhite-crowned sparrow song performance scriptWCSP_resubmissionScript.R
DOI: 10.5061/dryad.ft612j0h
title: Data from: Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: the Latent Environmental Threshold Model

description: Conditional strategies are the most common form of discrete phenotypic
 plasticity. In a conditional strategy, the phenotype expressed by an
 organism is determined by the difference between an environmental cue and
 a threshold, both of which may vary among individuals. The Environmental
 Threshold model (ETM) has been proposed as a mean to understand the
 evolution of conditional strategies, but has been surprisingly seldom
 applied to empirical studies. A hindrance for the application of the ETM
 is that often, the proximate cue triggering the phenotypic expression and
 the individual threshold are not measurable, and can only be assessed
 using a related observable cue. We describe a new statistical model that
 can be applied in this common situation. The Latent Environmental
 Threshold Model (LETM) allows for a measurement error in the phenotypic
 expression of the individual environmental cue and a purely genetically
 determined threshold. We show that coupling our model with quantitative
 genetic methods allows an evolutionary approach including an estimation of
 the heritability of conditional strategies. We evaluate the performance of
 the LETM with a simulation study and illustrate its utility by applying it
 to empirical data on the size-dependent smolting process for
 stream-dwelling Atlantic salmon juveniles.
description: Data_LETMThis data file contains: a script for simulated data sets using R software (ScriptR_LETM_SIM.R), a script (ScriptR_LETM_SAT.R) to analyze data collected in the field (Data_SAT.RData) using R and OpenBUGS software.LETM.zip
DOI: 10.5061/dryad.6rj0n
title: Data from: A global optimization paradigm based on change of measures

description: A global optimization framework, COMBEO (Change Of Measure Based
 Evolutionary Optimization), is proposed. An important aspect in the
 development is a set of derivative-free additive directional terms,
 obtainable through a change of measures en route to the imposition of any
 stipulated conditions aimed at driving the realized design variables
 (particles) to the global optimum. The generalized setting offered by the
 new approach also enables several basic ideas, used with other global
 search methods such as the particle swarm or the differential evolution,
 to be rationally incorporated in the proposed set-up via a change of
 measures. The global search may be further aided by imparting to the
 directional update terms additional layers of random perturbations such as
 ‘scrambling’ and ‘selection’. Depending on the precise choice of the
 optimality conditions and the extent of random perturbation, the search
 can be readily rendered either greedy or more exploratory. As numerically
 demonstrated, the new proposal appears to provide for a more rational,
 more accurate and, in some cases, a faster alternative to many available
 evolutionary optimization schemes.
description: exampleexperimentThis is the main file for solving global optimization problems. In this specific case pseudo-code 2 has been used for demonstrating the performance the algorithm. All the input values (i.e. dimension of problem, minimum and maximum function evaluations) are to be given here. To run this code, except the functions uploaded herein plese use the two function benchmarks.m and fgeneric.m from https://www.lri.fr/~hansen/cmaes_inmatlab.html which is an open sorce platform.MY_OPTIMIZERThe specific optimization algorithm is written here. For solving the global optimization problem with a different algorithm, only this function needs to be modified.new_KS_EnKF_gain_matrixThis function creates the gain matrix, defined in the main manuscript, which is required in pseudo code 2 for giving the evolving particle proper directionality.phase_KThe phase data (attached) for the illustrative example in Section 5.2phase_KThe phase data (attached) for the illustrative example in Section 5.2
DOI: 10.5061/dryad.0pq4t
title: Data from: Plant-herbivore interactions: silicon concentration in tussock sedges and population dynamics of root voles

description: 1. It has been hypothesized that the induction of silicon (Si)-based plant
 defence in response to herbivore damage may engender rodent population
 cycles. Many studies have also considered accumulation of Si as a process
 controlled by geo-hydrological factors. 2. To test these ideas, we
 investigated the relationship between concentration of Si in fibrous
 tussock sedge (Carex appropinquata) and the population density of a major
 sedge consumer, the root vole (Microtus oeconomus), in field enclosures in
 natural habitat under a variety of natural water regimes and weather
 conditions. 3. We found that a high density of voles at the end of summer
 resulted in the immediate accumulation of Si by rhizomes, followed by
 accumulation of Si in leaves with a one-year lag time. The level of river
 flooding in the same year had an additional impact on Si concentration in
 rhizomes but did not affect silicification of leaves. 4. Overwinter
 changes in concentration of Si in sedges were influenced by fluctuations
 in ambient temperature and the depth of snow cover (multiple freeze-thaw
 cycles), thus affecting the quality of winter food available for voles. 5.
 Smaller voles had lower mortality during early winter than large voles,
 which seemed to be connected with changes in the quality of the autumn
 rather than the winter food base. Winter survival of voles was not
 associated with Si concentration in their faeces, however. 6. Our results
 suggest that changes in Si concentration in fibrous tussock sedge can be
 induced by changes in vole population density and are also additionally
 affected by the amount of flooding and weather conditions.
description: Appendix
 S3Raw
 data for the model depicted in Figure 1Appendix S
 3.csvAppendix
 S4Raw
 data for the model depicted in Table 2Appendix
 S5Raw
 data for the model depicted in Figure 2Appendix
 S6Raw
 data for the model depicted in Table 3
DOI: 10.5061/dryad.pb62bk0
title: Data from: Grazing away the resilience of patterned ecosystems

description: Ecosystems’ responses to changing environmental conditions can be
 modulated by spatial self-organization. A prominent example of this can be
 found in drylands, where formation of vegetation patterns attenuates the
 magnitude of degradation events in response to decreasing rainfall. In
 model studies, the pattern wavelength responds to changing conditions,
 which is reflected by a rather gradual decline in biomass in response to
 decreasing rainfall. Although these models are spatially explicit, they
 have adopted a mean-field approach to grazing. By taking into account
 spatial variability when modelling grazing, we find that (over)grazing can
 lead to a dramatic shift in biomass, so that degradation occurs at
 rainfall rates that would otherwise still maintain a relatively productive
 ecosystem. Moreover, grazing increases the resilience of degraded
 ecosystem states. Consequently, restoration of degraded ecosystems could
 benefit from the introduction of temporary small-scale exclosures, to
 escape from the basin of attraction of degraded states.
description: GNU Octave/MATLAB model
 implementationThis file can be used to
 compute model runs as in Figure 2 from the publication.extKAmNat.mModel RunsData from model runs in Figure 2 and 3. Each of the five variables, umatFigxxxx, corresponds to a panel in Figure 2 or 3. Use imagesc(umatFigxxxx(:,:,2)) to see the vegetation component (as in the panels) and deduce the correspondence, and imagesc(umatFigxxxx(:,:,1)) for the water component of the Klausmeier model.ModelRunsAmNat.mat