cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3879g
title: Data from: The large-scale drivers of population declines in a long-distance migratory shorebird

description: Migratory species can travel tens of thousands of kilometers each year,
 spending different parts of their annual cycle in geographically distinct
 locations. Understanding the drivers of population change is vital for
 conserving migratory species, yet the challenge of collecting data over
 entire geographic ranges has hindered attempts to identify the processes
 leading to observed population changes. Here, we use remotely sensed
 environmental data and count data to investigate the factors driving
 variability in abundance in two subspecies of a long-distance migratory
 shorebird, the bar-tailed godwit (Limosa lapponica). We compiled a
 spatially and temporally explicit dataset of three environmental variables
 to identify the conditions experienced by each subspecies in each stage of
 their annual cycle (breeding, non-breeding and staging). We used a
 Bayesian N-mixture model to analyze 18 years of monthly count data from 21
 sites across Australia and New Zealand in relation to the remote sensing
 datasets. We found that the abundance of one subspecies (L. l. menzbieri)
 in their non-breeding range was related to climate conditions in breeding
 grounds, and detected sustained population declines between 1995 and 2012
 in both subspecies (L. l. menzbieri, -6.7% and L. l. baueri, -2.1%
 year-1). To investigate the possible causes of the declines, we quantified
 changes in habitat extent at 22 migratory staging sites in the Yellow Sea,
 East Asia, over a 25-year period and found -1.7% and -1.2% year-1 loss of
 habitat at staging sites used by L. l. menzbieri and L. l baueri,
 respectively. Our results highlight the need to identify environmental and
 anthropogenic drivers of population change across all stages of migration
 to allow the formulation of effective conservation strategies across
 entire migratory ranges.
description: JAGS code for the
 bar-tailed godwit population analysisbtgo.jags.txt
DOI: 10.5061/dryad.6m220kd
title: Data from: Mechanisms of reciprocity and diversity in social networks: a modelling and comparative approach

description: Three mechanisms have been proposed to underlie reciprocation of social
 behaviors in gregarious animals: ‘calculated reciprocity’, ‘emotional
 bookkeeping’ and ‘symmetry-based reciprocity’. Among these explanations,
 emotional book-keeping has received the broadest support from experimental
 and observational studies. On the other hand, three individual-based
 models have shown that reciprocation may emerge via ‘symmetry-based
 reciprocity’, ‘emotional bookkeeping’, or a combination of both
 mechanisms. Here we use these three models to assess their relative fit
 with empirical data on reciprocation and social network structure across
 different groups and species of macaques. We collected grooming data from
 14 groups and 8 macaque species and simulated each group in each model. We
 analyzed and quantitatively compared social network metrics of the
 empirical and the models’ grooming networks. The three models captured
 fairly well the features of observed networks, and fitted data from wild
 groups better than captive ones. The emotional bookkeeping model seemed on
 average to fit slightly better the social networks metrics observed in
 empirical data, but failed to reproduce some grooming patterns. The
 symmetry-based models, on the other hand, fitted better other network
 parameters (e.g. modularity). No model generally fitted the data better
 than the others, and the fit with some metrics (e.g. modularity,
 centralization index) was low even after optimization. Thus, our analyses
 indicate that in the models social interactions may be simpler than in
 reality and models may miss social processes (e.g. third-party awareness).
description: Grooming matrices of
 macaques groups related to this studyThis in an R file. To
 open it is needed the R statistical software program. The file contain two
 elements. Matrices: contains the grooming matrices used in the analysis of
 this study. References: contains the citation from for each group and
 matrix used in the study. The order of elements in each object are
 correspondent. To call an see the contents of an object type
 'Matrices' or 'References' and hit
 enter.GroomingMatricesPugaGonzalezetal.2018.RData
DOI: 10.5061/dryad.gm187
title: Data from: A test of male infanticide as a reproductive tactic in a cichlid fish

description: Infanticide and offspring cannibalism are taxonomically widespread
 phenomena. In some group-living species, a new dominant individual taking
 over a group can benefit from infanticide if doing so induces potential
 mates to become reproductively available sooner. Despite widespread
 observations of infanticide (i.e. egg cannibalism) among fishes, no study
 has investigated whether egg cannibalism occurs in fishes as a result of
 group takeovers, or how this type of cannibalism might be adaptive. Using
 the cooperatively breeding cichlid, Neolamprologus pulcher, we tested
 whether new unrelated males entering the dominant position in a social
 group were more likely to cannibalize eggs, and whether such cannibalism
 would shorten the interval until the female's next spawning. Females
 spawned again sooner if their broods were removed than if they were cared
 for. Egg cannibalism occurred frequently after a group takeover event, and
 was rarer if the original male remained with the group. While dominant
 breeder females were initially highly aggressive towards newcomer males
 that took over the group, the degree of resistance depended on relative
 body size differences between the new pair and, ultimately, female
 aggression did not prevent egg cannibalism. Egg cannibalism, however, did
 not shorten the duration until subsequent spawning, or increase fecundity
 during subsequent breeding in our laboratory setting. Our results show
 that infanticide as mediated through group takeovers is a taxonomically
 widespread behaviour.
description: Jindal et al.
 trial_dataJindal et al.
 brood_removal
DOI: 10.5061/dryad.4067d
title: Data from: Cladograms, phylogenies and the veracity of the conodont fossil record

description: Traditionally, conodont intrarelationships have been reconstructed
 following the evolutionary palaeontology paradigm, which lacks a formal
 methodology, renders hypotheses unrepeatable and takes little account of
 the imperfect nature of the fossil record. Cladistics provides a
 prescriptive approach to phylogeny reconstruction and, it is argued, a
 rigorous method of character analysis that is not incompatible with the
 aims of evolutionary palaeontology. To demonstrate this, we use the
 Silurian family Kockelellidae as an example of how cladistics can be used
 to reconstruct relative relationships, and how such hypotheses can be
 converted to phylogenies. We follow traditional, cladistic approaches to
 assessing the completeness of the fossil record and find that failure to
 conduct this within a milieu of absolute, rather than merely relative,
 relationships leads to spurious inferences of gaps in the fossil record.
 This appears to be a problem that is widespread in theory, but peculiar to
 species in practice, and parallels the observation that cladograms of
 fossil species tend to exhibit poorer correlation to stratigraphy than do
 cladograms of fossil higher taxa. We conclude that cladistics provides the
 only appropriate framework within which to conduct character analysis;
 phylogenies can be developed from cladograms but very often this
 additional inferential step is entirely superfluous to the aims of
 evolutionary studies.
description: Cladistic data
 matrixCladistic data
 matrixKockelella
 matrix
DOI: 10.5061/dryad.3f4014q
title: Data from: Impacts of urbanization on insect herbivory and plant defences in oak trees

description: Systematic comparisons of species interactions in urban vs. rural
 environments can improve our understanding of shifts in ecological
 processes due to urbanization. However, such studies are relatively
 uncommon and the mechanisms driving urbanization effects on species
 interactions (e.g., between plants and insect herbivores) remain elusive.
 Here we investigated the effects of urbanization on leaf herbivory by
 insect chewers and miners associated with the English oak (Quercus robur)
 by sampling trees in rural and urban areas throughout most of the
 latitudinal distribution of this species. In performing these comparisons,
 we also controlled for the size of the urban areas (18 cities) and
 gathered data on CO2 emissions. In addition, we assessed whether
 urbanization affected leaf chemical defences (phenolic compounds) and
 nutritional traits (phosphorus and nitrogen), and whether such changes
 correlated with herbivory levels. Urbanization significantly reduced leaf
 chewer damage but did not affect leaf miners. In addition, we found that
 leaves from urban locations had lower levels of chemical defences
 (condensed and hydrolysable tannins) and higher levels of nutrients
 (nitrogen and phosphorus) compared to leaves in rural locations. The
 magnitude of urbanization effects on herbivory and leaf defences was not
 contingent upon city size. Importantly, while the effects of urbanization
 on chemical defences were associated with CO2 emissions, changes in leaf
 chewer damage were not associated with either leaf traits or CO2 levels.
 These results suggest that effects of urbanization on herbivory occur
 through mechanisms other than changes in the plant traits measured here.
 Overall, our simultaneous assessment of insect herbivory, plant traits,
 and abiotic correlates advances our understanding of the main drivers of
 urbanization effects on plant-herbivore interactions.
description: data_Moreira et
 al_2018
DOI: 10.5061/dryad.4t157
title: Data from: Ancestral character estimation under the threshold model from quantitative genetics

description: Evolutionary biology is a study of life's history on Earth. In
 researching this history, biologists are often interested in attempting to
 reconstruct phenotypes for the long extinct ancestors of living species.
 Various methods have been developed to do this on a phylogeny from the
 data for extant taxa. In the present article, I introduce a new approach
 for ancestral character estimation for discretely valued traits. This
 approach is based on the threshold model from evolutionary quantitative
 genetics. Under the threshold model, the value exhibited by an individual
 or species for a discrete character is determined by an underlying,
 unobserved continuous trait called “liability.” In this new method for
 ancestral state reconstruction, I use Bayesian Markov chain Monte Carlo
 (MCMC) to sample the liabilities of ancestral and tip species, and the
 relative positions of two or more thresholds, from their joint posterior
 probability distribution. Using data simulated under the model, I find
 that the method has very good performance in ancestral character
 estimation. Use of the threshold model for ancestral state reconstruction
 relies on a priori specification of the order of the discrete character
 states along the liability axis. I test the use of a Bayesian MCMC
 information theoretic criterion based approach to choose among different
 hypothesized orderings for the discrete character. Finally, I apply the
 method to the evolution of feeding mode in centrarchid fishes.
description: All code &
 scriptsThis zipped tarball
 contains all the code & scripts necessary (combined with R packages
 available through CRAN) to reproduce the analyses of this study. All files
 are plain text and contain a short description of the specific analysis or
 analyses that will be generated by the script.Revell-ancThresh.tar.gz
DOI: 10.5061/dryad.9s364g3
title: Data from: Morphological adaptations for relatively larger brains in hummingbird skulls

description: A common allometric pattern called Haller’s Rule states that small species
 have relatively larger brains and eyes than larger species of the same
 taxonomic group. This pattern imposes drastic structural changes and
 energetic costs on small species to produce and maintain a
 disproportionate amount of nervous tissue. Indeed, several studies have
 shown the significant metabolic costs of having relatively larger brains;
 however, little is known about the structural constraints and adaptations
 required for housing these relatively larger brains and eyes. Because
 hummingbirds include the smallest birds, they are ideal for exploring how
 small species evolve morphological adaptations for housing relatively
 larger brain and eyes. We here present results from a comparative study of
 hummingbirds and show that the smallest species have the lowest levels of
 ossification, the most compact braincases, and relatively larger eye
 sockets, but lower eye/head proportion, than larger species. In contrast
 to Passerines, skull ossification in hummingbirds correlates with body and
 brain size but not with age. Correlation of these skull traits with body
 size might represent adaptations to facilitate housing relatively larger
 brain and eyes, rather than just heterochronic effects related to change
 in body size. These structural changes in skull traits allow small animals
 to accommodate disproportionately larger brains and eyes without further
 increasing overall head size.
description: Ossification
 dataThis file has the
 average body mass and ossification data for 96 species of hummingbirds
 collected from museum specimensHummingbird skull
 morphology dataThis file has the
 average values of 6 morphological traits for 32 species of hummingbirds
 collected from museum specimens
DOI: 10.5281/zenodo.17980776
title: SHM_415339_HST_3D

description: Photogrammetric 3D model of an Early Neolithic polygonal axe collected from Sweden in 1858 and currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=706

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/0FB1414D-680D-49B1-94E5-A993A5DE4BB0
DOI: 10.5281/zenodo.17980775
title: SHM_415339_HST_3D

description: Photogrammetric 3D model of an Early Neolithic polygonal axe collected from Sweden in 1858 and currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=706

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/0FB1414D-680D-49B1-94E5-A993A5DE4BB0
DOI: 10.5061/dryad.12477
title: Data from: Nutrient availability and atmospheric CO2 partial pressure modulate the effects of nutrient heterogeneity on the size structure of populations in grassland species

description: Background and Aims: Size-asymmetric competition occurs when larger plants
 have a disproportionate advantage in competition with smaller plants. It
 has been hypothesized that nutrient heterogeneity may promote it.
 Experiments testing this hypothesis are inconclusive, and in most cases
 have evaluated the effects of nutrient heterogeneity separately from other
 environmental factors. The aim of this study was to test, using
 populations of Lolium perenne, Plantago lanceolata and Holcus lanatus, two
 hypotheses: (a) nutrient heterogeneity promotes size-asymmetric
 competition; and (b) nutrient heterogeneity interacts with both
 atmospheric CO2 partial pressure (PCO2) and nutrient availability to
 determine the magnitude of this response. Methods: Microcosms consisting
 of monocultures of the three species were grown for 90 d in a factorial
 experiment with the following treatments: PCO2 (37 5 and 70 Pa) and
 nutrient availability (NA; 40 and 120 mg of N added as organic material)
 combined with different spatial distribution of the organic material (NH;
 homogeneous and heterogeneous). Differences in the size of individual
 plants within populations (size inequality) were quantified using the
 coefficient of variation of individual above-ground biomass and the
 combined biomass of the two largest individuals in each microcosm.
 Increases in size inequality were associated with size-asymmetric
 competition. Key Results: Size inequality increased when the nutrients
 were heterogeneously supplied in the three species. The effects of NH on
 this response were more pronounced under high nutrient supply in both
 Plantago and Holcus (significant NA x NH interactions) and under elevated
 PCO2 in Plantago (significant PCO2 x NA x NH interaction). No significant
 two- and three-way interactions were found for Lolium. Conclusions: Our
 first hypothesis was supported by our results, as nutrient heterogeneity
 promoted size-asymmetric competition in the three species evaluated.
 Nutrient supply and PCO2 modified the magnitude of this effect in Plantago
 and Holcus, but not in Lolium. Thus, our second hypothesis was partially
 supported.
description: Data on individual
 biomass and root proliferation into nutrient patchesAboveground biomass per
 individual and root proliferation into nutrient pathces at the moment of
 harvest.Ann_Bot_2006.zip
DOI: 10.5061/dryad.1750
title: Data from: Historical mutation rates predict susceptibility to radiation in Chernobyl birds

description: Extreme environmental perturbations are rare, but may have important
 evolutionary consequences. Responses to current perturbations may provide
 important information about the ability of living organisms to cope with
 similar conditions in the evolutionary past. Radioactive contamination
 from Chernobyl constitutes one such extreme perturbation, with significant
 but highly variable impact on local population density and mutation rates
 of different species of animals and plants. We explicitly tested the
 hypothesis that species with strong impacts of radiation on abundance were
 those with high rates of historical mutation accumulation as reflected by
 cytochrome b mitochondrial DNA base pair substitution rates during past
 environmental perturbations. Using a dataset of 32 species of birds we
 show higher historical mitochondrial substitution rates in species with
 the strongest negative impact of local levels of radiation on local
 population density. These effects were robust to different estimates of
 impact of radiation on abundance, weighting of estimates of abundance by
 sample size, statistical control for similarity in the response among
 species due to common phylogenetic descent, and effects of population size
 and longevity. Therefore, species that respond strongly to the impact of
 radiation from Chernobyl are also the species that in the past have been
 most susceptible to factors that have caused high substitution rates in
 mitochondrial DNA.
description: ChernobylData.txtDatafile containing all information as defined in paper
DOI: 10.5281/zenodo.18382939
title: WSTD : WEB-APPLICATION SECURITY TRAFFIC DATASET

description: This Repository consist of  6 PCAP files captured using the Wireshark tool within the fully isolated virtual lab environment. All experiments were conducted on virtual machines using private IP addresses, VM-assigned MAC addresses, and default test credentials from a vulnerable web application, and this Dataset includes no real user data or production network traffic. Access to the files is restricted upon request, as the captures contain clear-text authentication data and tokens associated only with controlled test accounts.
DOI: 10.5281/zenodo.18382940
title: WSTD : WEB-APPLICATION SECURITY TRAFFIC DATASET

description: This Repository consist of  6 PCAP files captured using the Wireshark tool within the fully isolated virtual lab environment. All experiments were conducted on virtual machines using private IP addresses, VM-assigned MAC addresses, and default test credentials from a vulnerable web application, and this Dataset includes no real user data or production network traffic. Access to the files is restricted upon request, as the captures contain clear-text authentication data and tokens associated only with controlled test accounts.
DOI: 10.5061/dryad.s4k1q
title: Data from: Tracing coco de mer’s reproductive history: pollen and nutrient limitation reduce fecundity

description: Habitat degradation can reduce or even prevent the reproduction of
 previously abundant plant species. To develop appropriate management
 strategies, we need to understand the reasons for reduced recruitment in
 degraded ecosystems. The dioecious coco de mer palm (Lodoicea maldivica)
 produces by far the largest seeds of any plant. It is a keystone species
 in an ancient palm forest that occurs only on two small islands in the
 Seychelles, yet contemporary rates of seed production are low, especially
 in fragmented populations. We developed a method to infer the recent
 reproductive history of female trees from morphological evidence present
 on their inflorescences. We then investigated the effects of habitat
 disturbance and soil nutrient conditions on flower and fruit production.
 The 57 female trees in our sample showed a 19.5-fold variation in flower
 production among individuals over a seven-year period. Only 77.2% of trees
 bore developing fruits (or had recently shed fruits), with the number per
 tree ranging from zero to 43. Flower production was positively correlated
 with concentrations of available soil nitrogen and potassium, and did not
 differ significantly between closed and degraded habitat. Fruiting success
 was positively correlated with pollen availability, as measured by numbers
 and distance of neighbouring male trees. Fruit-set was lower in degraded
 habitat than in closed forest, while the proportion of abnormal fruits
 that failed to develop was higher in degraded habitat. Seed size recorded
 for a large sample of seeds varied widely, with fresh weights ranging from
 1 to 18 kg. Shortages of both nutrients and pollen appear to limit seed
 production of Lodoicea in its natural habitat, with these factors
 affecting different stages of the reproductive process. Flower production
 varies widely amongst trees, while seed production is especially low in
 degraded habitat. The size of seeds is also very variable. We discuss the
 implications of these findings for managing this ecologically and
 economically important species.
description: Lodoicea maldivica
 individual female fecundity, and nutrient, pollen and genetic
 factors170109_fecundity_DRYAD.txt