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26 Research products, page 1 of 3

  • Digital Humanities and Cultural Heritage
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  • Open Access
    Authors: 
    Li, Bochen; Liu, Xinzhao; Dinesh, Karthik; Duan, Zhiyao; Sharma, Gaurav;
    Country: Netherlands

    We introduce a dataset for facilitating audio-visual analysis of musical performances. The dataset comprises 44 simple multi-instrument classical music pieces assembled from coordinated but separately recorded performances of individual tracks. For each piece, we provide the musical score in MIDI format, the audio recordings of the individual tracks, the audio and video recording of the assembled mixture, and ground- truth annotation files including frame-level and note-level tran- scriptions. We describe our methodology for the creation of the dataset, particularly highlighting our approaches for addressing the challenges involved in maintaining synchronization and ex- pressiveness. We demonstrate the high quality of synchronization achieved with our proposed approach by comparing the dataset against existing widely-used music audio datasets. We anticipate that the dataset will be useful for the devel- opment and evaluation of existing music information retrieval (MIR) tasks, as well as for novel multi-modal tasks. We bench- mark two existing MIR tasks (multi-pitch analysis and score- informed source separation) on the dataset and compare against other existing music audio datasets. Additionally, we consider two novel multi-modal MIR tasks (visually informed multi-pitch analysis and polyphonic vibrato analysis) enabled by the dataset and provide evaluation measures and baseline systems for future comparisons (from our recent work). Finally, we propose several emerging research directions that the dataset enables. URMP DatasetWe introduce a dataset for facilitating audio-visual analysis of musical performances. The dataset comprises a number of simple multi-instrument musical pieces assembled from coordinated but separately recorded performances of individual tracks. For each piece, we provide the musical score in MIDI format, the high-quality individual instrument audio recordings and the videos of the assembled pieces. We anticipate that the dataset will be useful for multi-modal information retrieval techniques such as music source separation, transcription, performance analysis and also serve as ground-truth for evaluating performances.Dataset.tar.gz

  • Open Access
    Authors: 
    Bell, Mark A.; Lloyd, Graeme T.;
    Publisher: Data Archiving and Networked Services (DANS)
    Country: Netherlands

    strap (Stratigraphic Tree Analysis for Palaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time-scale phylogenies of fossil taxa; (2) to plot those time-scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time-scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scaless is possible using the geoscalePhylo function. Finally, the function StratPhyloCongruence calculates stratigraphic congruence measures for one or more input phylogenies, with no taxon limit. All three major congruence measures are offered: Stratigraphic Consistency Index (SCI), Manhattan Stratigraphic Measure (MSM*) and the gap excess ratio (GER; including GERt and GER*), as well as the pseudocongruence measure, the Relative Completeness Index (RCI). Each measure has an accompanying significance test that works by comparing the input trees against a user-defined number of randomly generated topologies with the same taxon set and age ranges. Additional options for generating these random topologies allow the user to fix the outgroup or retain the input tree shape to make fairer comparisons. A tutorial that assumes no prior knowledge of R showcases all three functions using two different example data sets. Dipnoi treeThe single favoured MPT from Lloyd et al., 2012.Dipnoi.treDipnoi agesUpper and lower bounds from the first appearance for the taxa in the tree contained in Dipnoi.tre.Dipnoi.txtAsaphidae treesAll 162 MPTs of the trilobite Family Asaphidae from Bell and Braddy, 2012.Asaphidae.treAsaphidae stratigraphic rangesFirst and last appearance datums for all species within the Asaphidae.tre file.Asaphidae.txtBell and Lloyd - Strap tutorialTutorial describing usage of main functions of strap (v 1.4) package for R.Bell and Lloyd - SI Tutorial.pdf

  • Open Access English
    Authors: 
    Rydell, Jens; Eklöf, Johan; Sanchez Navarro, Sonia;
    Publisher: Dryad
    Country: Netherlands

    We surveyed 110 country churches in south-western Sweden for presence of brown long-eared bats Plecotus auritus in summer 2016 by visual inspection and/or evening emergence counts. Each church was also classified according to the presence and amount of aesthetic directional lights (flood-lights) aimed on its walls and tower from the outside. Sixty-one of the churches had previously been surveyed by one of us (J.R.) between 1980 and 1990, before lights were installed on Swedish churches, using the same methods. Churches with bat colonies had decreased significantly in frequency from 61% in 1980s to 38% by 2016. All abandoned churches had been fitted with flood-lights in the period between the two surveys. The loss of bat colonies from lit churches was highly significant and most obvious when lights were applied from all directions, leaving no dark corridor for the bats to leave and return to the roost. In contrast, in churches that were not lit, all of 13 bat colonies remained after 25+ years between the surveys. Lighting of churches and other historical buildings is a serious threat to the long-term survival and reproduction of light-averse bats such as Plecotus spp. and other slow-flying species. Bat roosts are strictly protected according to the EU Habitats Directive and the EUROBATS agreement. Lighting of buildings for aesthetic purposes is becoming a serious environmental issue, because important bat roosts are destroyed in large numbers, and the problem should be handled accordingly. As a start, installation of flood-lights on historical buildings should at least require an environmental impact assessment (EIA). Rydell et al. Age of enlightenment. Supplementary data.Basic data data on churches. Frequency of bat occurrence and information on lights and renovations.Rydell et al churches.xlsx

  • Open Access
    Authors: 
    Arkle, Kelsey M.; Miller, Arnold I.;
    Publisher: Data Archiving and Networked Services (DANS)
    Country: Netherlands

    Death Assemblage - Arkle 2017Raw abundances of death assemblage data from seven localities around St. Croix, USVI. Singletons have been removed and bivalve abundances have been halved to provide a minimum number of individuals (MNI). First two letters in row names (sites) indicate locality (SC=Smuggler's Cove, CH=Christiansted Harbor, PP=Power Plant, SR=Salt River Bay, MP=Molasses Pier, HP=Ha'Penny Bay, DS=Dump Site). First set of numbers in sample labels indicate position on the transect (in meters). Letters B,C, and D indicate depth (see text), and numbers 11 and 12 indicate sampling years (2011 and 2012, respectively). Columns are species names.Arkle_Dead_FINAL.xlsxLife Assemblage - Arkle 2017Raw abundances of life assemblage data from seven localities around St. Croix, USVI. Singletons have been removed. First two letters in row names (sites) indicate locality (SC=Smuggler's Cove, CH=Christiansted Harbor, PP=Power Plant, SR=Salt River Bay, MP=Molasses Pier, HP=Ha'Penny Bay, DS=Dump Site). First set of numbers in sample labels indicate position on the transect (in meters). Letter A indicates that all are living individuals, and numbers 11 and 12 indicate sampling years (2011 and 2012, respectively). Columns are species names.Arkle_Live_Final.xlsxSeagrass Census - Arkle 2017Average seagrass and macroalgal abundances from seven localities around St. Croix, USVI. First two letters in row names (sites) indicate locality (SC=Smuggler's Cove, CH=Christiansted Harbor, PP=Power Plant, SR=Salt River Bay, MP=Molasses Pier, HP=Ha'Penny Bay, DS=Dump Site). First set of numbers in sample labels indicate position on the transect (in meters), and numbers 11 and 12 indicate sampling years (2011 and 2012, respectively). Columns are species names.Arkle_Seagrass_FINAL.xlsx Death assemblages that occupy the upper tens of centimeters of sediment in shallow-marine settings are often subject to extensive mixing, thereby limiting their usefulness in assessing environmentally mediated compositional changes through time in the local biota. Here, we provide evidence that dense, Thalassia-rich seagrass beds preserve a stratigraphic record of biotic variation because their dense root–rhizome mats inhibit mixing. We sampled benthic mollusk assemblages at seven localities in Thalassia-rich beds around St. Croix, USVI, collecting three separate sediment intervals of ~13 cm each to a total depth of ~40 cm below the sediment–water interface, and found evidence that sedimentary intervals preserved compositional stratigraphy. Further, some localities displayed systematic, directional changes down-core. An examination of interval-to-interval changes in composition revealed that compositional variation was unique from locality to locality rather than reflecting coordinated, island-wide transitions. In general, however, relative abundances of epifaunal gastropods and small lucinid bivalves tended to decrease with depth below the sediment–water interface. Quantitative comparisons of life-to-death assemblages from each successive sedimentary interval demonstrated that the shallowest death assemblages were typically more similar to the life assemblages than were deeper assemblages, suggesting that deeper intervals provide records of earlier community states.

  • Open Access
    Authors: 
    Carrillo, Juan D.; Amson, Eli; Jaramillo, Carlos; Sánchez, Rodolfo; Quiroz, Luis; Cuartas, Carlos; Rincón, Aldo F.; Sánchez-Villagra, Marcelo Ricardo;
    Publisher: Data Archiving and Networked Services (DANS)
    Country: Netherlands

    South America was isolated during most of the Cenozoic, and it was home to an endemic fauna. The South American Native Ungulates (SANUs) exhibited high taxonomical, morphological, and ecological diversity and were widely distributed on the continent. However, most SANU fossil records come from high latitudes. This sampling bias challenges the study of their diversity dynamics and biogeography during important tectonic and biotic events, such as the Great American Biotic Interchange, the faunal exchange between North and South America after the formation of the Isthmus of Panama. We describe new SANU remains from the Neogene of the Cocinetas (northern Colombia) and Falcón (northwestern Venezuela) Basins. In the Cocinetas Basin, the middle Miocene fauna of the Castilletes Formation includes Hilarcotherium miyou sp. nov. (Astrapotheriidae), cf. Huilatherium (Leontiniidae), and Lambdaconus cf. L. colombianus (Proterotheriidae). The late Pliocene fauna of the Ware Formation includes a Toxodontinae indet. and the putative oldest record of Camelidae in South America. In the Falcón Basin, the Pliocene/Pleistocene faunas of the Codore and San Gregorio Formations include Falcontoxodon aguilerai gen. et sp. nov. and Proterotheriidae indet. We provide a phylogenetic analysis for Astrapotheriidae and Toxodontidae. The new data document a low-latitude provinciality within some SANU clades (e.g., Astrapotheriidae, Leontiniidae) during the middle Miocene. This contrasts with the wide latitudinal distribution of clades of other mammals recorded in the fauna, including the sparassodont Lycopsis padillai, the sloth Hyperleptus, and the proterotheriid Lambdaconus cf. L. colombianus. Appendix 1. Stratigraphic description of ten sections and their geographical locationThis file contains a detailed lithological description and geographic position of ten stratigraphic sections in the Falcón basin. These sections encompass the entire Neogene sequence.Appendix 1.zipAppendix 2. Detailed description of each of the studies used to define the chronostratigraphy of the Urumaco regionThis files provides a detailed description of each of the studies used to define the chronostratigraphy of the Urumaco regionAppendix 2.xlsAppendix 3. Character-taxon matrix used in the phylogenetic analysis of AstrapotheriidaeNexus file with the annotated character-taxon matrix used in the phylogenetic analysis of Astrapotheriidae. It includes the commands use in the analysis with PAUPAppendix 3.nexAppendix 4. Character-taxon matrix used in the phylogenetic analysis of Toxodontidae.Nexus file with the annotated character-taxon matrix used in the phylogenetic analysis of Toxodontidae. It includes the commands for the analysis in PAUP under equal weightsAppendix 4 equal weights.nexAppendix 4. Character-taxon matrix used in the phylogenetic analysis of ToxodontidaeNexus file with the annotated character-taxon matrix used in the phylogenetic analysis of Toxodontidae. It includes the commands for the analysis in PAUP using implied weightingAppendix 4 goloboff.nex

  • Open Access
    Authors: 
    Brochu, Christopher A.;
    Publisher: Zenodo
    Country: Netherlands

    Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved. Brochu Data Setbrochu.mc

  • Open Access
    Authors: 
    Herrera, James;
    Publisher: Dryad Digital Repository
    Country: Netherlands

    Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ~600 fossil species and 90% complete phylogenies of living species: 1) diversification rates increased through time; 2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies consistently supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ~34 Ma, but also elevated extinction ~10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses. Supplementary MaterialsAppendix to accompany the manuscript: Primate diversification dynamics inferred from fossils and phylogenies.Supplementary materials for Primate diversification round 3.docxTable S1. Model fit resultsTable S1. Full results of RPANDA model comparisons with four different time-calibrated trees.Raw data on fossil taxonomy and agesRaw data on fossil taxonomy, first and last appearance dates (FAD, LAD, respectively), and number of occurrences, with ages and references from PBDB and the literature search performed in this study.Table S3. Raw data on fossils.xlsxTable S4. PBDB raw dataRaw data and references downloaded from Paleobiology DatabaseR code for Herrera Primate diversificationR code to run RPANDA phylogenetic diversification analysis, and fossil data preparation for PYRATE as well as analyses with PALEOTREEPhylogenetic trees from Springer et al. 2012Raw tree files of four phylogenetic trees from Springer et al. 2012 for all primates with different age calibration assumptionsspringer_trees.tre

  • Open Access
    Authors: 
    Kai, Zhong; Woan, Teoh Shu; Jie, Li; Goodale, Eben; Kitajima, Kaoru; Bagchi, Robert; Harrison, Rhett D.; Kai, Zhang;
    Country: Netherlands

    The value of local ecological knowledge (LEK) to conservation is increasingly recognised, but LEK is being rapidly lost as indigenous livelihoods change. Biodiversity loss is also a driver of the loss of LEK, but quantitative study is lacking. In our study landscape in SW China, a large proportion of species have been extirpated. Hence, we were interested to understand whether species extirpation might have led to an erosion of LEK and the implications this might have for conservation. So we investigated peoples' ability to name a selection of birds and mammals in their local language from pictures. Age was correlated to frequency of forest visits as a teenager and is likely to be closely correlated to other known drivers of the loss of LEK, such as declining forest dependence. We found men were better at identifying birds overall and that older people were better able to identify birds to the species as compared to group levels (approximately equivalent to genus). The effect of age was also stronger among women. However, after controlling for these factors, species abundance was by far the most important parameter in determining peoples' ability to name birds. People were unable to name any locally extirpated birds at the species level. However, contrary to expectations, people were better able to identify extirpated mammals at the species level than extant ones. However, extirpated mammals tend to be more charismatic species and several respondents indicated they were only familiar with them through TV documentaries. Younger people today cannot experience the sights and sounds of forest animals that their parents grew up with and, consequently, knowledge of these species is passing from cultural memory. We suggest that engaging older members of the community and linking the preservation of LEK to biodiversity conservation may help generate support for conservation. Analysis codeR code for analysis conducted in our studyAnalysis_final.RData file for birdsComma separated text file of the bird dataBirds.csvData file for mammalsComma separated text file of mammal dataMammals.csv

  • Open Access English
    Authors: 
    Fitzpatrick, Matthew C.; Sanders, Nathan J.; Normand, Signe; Svenning, Jens-Christian; Ferrier, Simon; Gove, Aaron D.; Dunn, Robert R.; Sanders, N. J.; Normand, S.; Dunn, R. R.; +3 more
    Publisher: Dryad
    Country: Netherlands

    A common approach for analysing geographical variation in biodiversity involves using linear models to determine the rate at which species similarity declines with geographical or environmental distance and comparing this rate among regions, taxa or communities. Implicit in this approach are weakly justified assumptions that the rate of species turnover remains constant along gradients and that this rate can therefore serve as a means to compare ecological systems. We use generalized dissimilarity modelling, a novel method that accommodates variation in rates of species turnover along gradients and between different gradients, to compare environmental and spatial controls on the floras of two regions with contrasting evolutionary and climatic histories: southwest Australia and northern Europe. We find stronger signals of climate history in the northern European flora and demonstrate that variation in rates of species turnover is persistent across regions, taxa and different gradients. Such variation may represent an important but often overlooked component of biodiversity that complicates comparisons of distance–decay relationships and underscores the importance of using methods that accommodate the curvilinear relationships expected when modelling beta diversity. Determining how rates of species turnover vary along and between gradients is relevant to understanding the sensitivity of ecological systems to environmental change. Plant species distribution, seed dispersal traits, and environmental data for southwest AustraliaPlant distribution data from the Western Australia Herbarium. Environmental data from worldclim (climate) and the Australian Natural Resources Data Library (soils). See publication for details.SWWA.env.spp.dat.csvPlant species distribution, seed dispersal traits, and environmental data for northern EuropePlant distribution data from Atlas Florae Europaeae. Environmental data from worldclim (climate) and, for soils, Batjes, N. H. 1997 A world dataset of derived soil properties by FAO–UNESCO soil unit for global modelling. Soil Use and Management 13, 9–16. See publication for details.NOR_EU.env.spp.dat.csvR scripts used to perform analyses described in journal article.Annotated R scripts required to run GDM on plant distribution data.code4public_allAnalyses.R

  • Open Access
    Authors: 
    Rivals, Florent; Prignano, Luce; Semprebon, Gina M.; Lozano, Sergi;
    Publisher: Zenodo
    Country: Netherlands

    DATASET 1 - EXTANT UNGULATESDataset of tooth microwear patterns in large samples of 10 extant ungulate populations with good records of the date and conditions of death.DATASET 2 - ARCHAEOLOGICAL SAMPLESDataset of tooth microwear patterns in archaeological samples of ungulates from five Middle and Late Pleistocene localities in Europe.Boundaries with transparent grid​Transparent grid to be superimposed to the heat map for positioning new samples according the SD and CV values.Background with boundaries and error probabilityBoundary lines with the error probability (heat map) based on SD and CV values of microwear data used for the classification of samples into short events (region 1​), long-continued events (region 2), or two separated short events (region 3​).Background_with_boundaries_and_error_probability.tiffg12.datBoundary between region 1 (short mortality events) and region 2 (longer mortality evens). The coordinates x (CV) and y (SD) of the points belonging to the curve have been calculated numerically for x in [0:1] and y in [0:10] and are reported in two columns with a space as separator.g23.datBoundary between region 2 (longer than seasonal mortality events) and region 3 (two separated mortality evens). The coordinates x (CV) and y (SD) of the points belonging to the curve have been calculated numerically for x in [0:1] and y in [0:10] and are reported in two columns with a space as separator. Since the curve is not continuous, there is a blank line separating the two branches.var.datError probability in the range CV=[0:1], SD=[1:10]. The values have been calculated numerically and are reported in three columns (CV, SD and the error probability value, respectively) with a space as separator. The step separating the values of CV is dCV=0.01 and that of SD is dSD=0.01. The seasonality of human occupations in archaeological sites is highly significant for the study of hominin behavioural ecology, in particular the hunting strategies for their main prey-ungulates. We propose a new tool to quantify such seasonality from tooth microwear patterns in a dataset of ten large samples of extant ungulates resulting from well-known mass mortality events. The tool is based on the combination of two measures of variability of scratch density, namely standard deviation and coefficient of variation. The integration of these two measurements of variability permits the classification of each case into one of the following three categories: (1) short events, (2) long-continued event and (3) two separated short events. The tool is tested on a selection of eleven fossil samples from five Palaeolithic localities in Western Europe which show a consistent classification in the three categories. The tool proposed here opens new doors to investigate seasonal patterns of ungulate accumulations in archaeological sites using non-destructive sampling.