cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x95x69pgf
title: Data from: The influence of climate variability on demographic rates of avian Afro-palearctic migrants

description: Climate is an important driver of changes in animal population size, but
 its effect on the underlying demographic rates remains insufficiently
 understood. This is particularly true for avian long-distance migrants
 which are exposed to different climatic factors at different phases of
 their annual cycle. To fill this knowledge gap, we used data collected by
 a national-wide bird ringing scheme for eight migratory species wintering
 in sub-Saharan Africa and investigated the impact of climate variability
 on their breeding productivity and adult survival. While temperature at
 the breeding grounds could relate to the breeding productivity either
 positively (higher food availability in warmer springs) or negatively
 (food scarcity in warmer springs due to trophic mismatch), water
 availability at the non-breeding should limit the adult survival and the
 breeding productivity. Consistent with the prediction of the trophic
 mismatch hypothesis, we found that warmer springs at the breeding grounds
 were linked with lower breeding productivity, explaining 29% of temporal
 variance across all species. Higher water availability at the sub-Saharan
 non-breeding grounds was related to higher adult survival (18% temporal
 variance explained) but did not carry-over to breeding productivity. Our
 results show that climate variability at both breeding and non-breeding
 grounds shapes different demographic rates of long-distance migrants.
DOI: 10.5061/dryad.m63xsj40j
title: Supplementary information from: Species interactions have predictable impacts on diversification

description: A fundamental goal of ecology is to reveal generalities in the myriad
 types of interactions among species, such as competition, mutualism, and
 predation. Another goal is to explain the enormous differences in species
 richness among groups of organisms. Here, we show how these two goals are
 intertwined: we find that different types of species interactions have
 predictable impacts on rates of species diversification, which underlie
 richness patterns. Based on a systematic review, we show that interactions
 with positive fitness effects for individuals of a clade (e.g. insect
 pollination for plants) generally increase that clade’s diversification
 rates. Conversely, we find that interactions with negative fitness effects
 (e.g. predation for prey, competition) generally decrease diversification
 rates. The sampled clades incorporate all animals and land plants,
 encompassing ~90% of all described species across life. Overall, we show
 that different types of local-scale species interactions can predictably
 impact large-scale patterns of diversification and richness.
DOI: 10.5061/dryad.qz612jmd0
title: Long-term cloud forest response to climate warming revealed by insect speciation history

description: Montane cloud forests are areas of high endemism, and are one of the more
 vulnerable terrestrial ecosystems to climate change. Thus, understanding
 how they both contribute to the generation of biodiversity, and will
 respond to ongoing climate change, are important and related challenges.
 The widely accepted model for montane cloud forest dynamics involves
 upslope forcing of their range limits with global climate warming.
 However, limited climate data provides some support for an alternative
 model, where range limits are forced downslope with climate warming.
 Testing between these two models is challenging, due to the inherent
 limitations of climate and pollen records. We overcome this with an
 alternative source of historical information, testing between competing
 model predictions using genomic data and demographic analyses for a
 species of beetle tightly associated to an oceanic island cloud forest.
 Results unequivocally support the alternative model: populations that were
 isolated at higher elevation peaks during the Last Glacial Maximum are now
 in contact and hybridising at lower elevations. Our results suggest that
 genomic data is a rich source of information to further understand how
 montane cloud forest biodiversity originates, and how it is likely to be
 impacted by ongoing climate change.
DOI: 10.82294/dvny3bkd6
title: Datos consolidados de eje medular. Territorio: Cartagena. Eje medular: Agenciamiento. Sector: Cultura, Educación, Total. Año: 2025

description: Datos consolidados de las observaciones semiestructuradas sobre el eje medular de agenciamiento, realizadas en la ciudad de Cartagena. Este dataset reúne los archivos correspondientes a los educadores artísticos del sector Educación y del sector Cultura, así como un archivo consolidado que integra la información de ambos sectores.
DOI: 10.5061/dryad.cc2fqz64j
title: Raw data: Soil microbes drive aboveground plant–pathogen–insect interactions

description: Plants interact with a large diversity of microbes and insects, both below
 and above ground. While studies have shown that belowground microbes
 affect the performance of plants and aboveground organisms, we lack
 insights into how belowground microbial communities may shape interactions
 between aboveground pathogens and insects. We investigated how soil
 microbiomes and aboveground organisms affect plant growth and development,
 and whether differences in soil microbiomes influence interactions between
 aboveground organisms. We conducted a growth-chamber experiment with oak
 seedlings (Quercus robur) growing in three soils with similar abiotic soil
 properties but with distinct natural soil microbiomes. Seedlings
 were subjected to single or dual attack by powdery mildew (Erysiphe
 alphitoides) and aphids (Tuberculatus annulatus), either in the presence
 or absence of prior attack by a free-feeding caterpillar (Phalera
 bucephala). Soil microbiomes were associated with differences in
 seedling height, and seedlings with multiple aboveground organisms had
 more but smaller leaves than healthy seedlings. The soil microbiome
 affected the severity of powdery mildew infection, and mediated the impact
 of co-occurring aboveground organisms on aphid population size. Our study
 highlights that plant performance is affected by natural soil microbiomes
 as well as aboveground organisms, and that natural soil microbiomes can
 affect interactions between pathogens and insects. These findings are
 important to understand species interactions in natural systems, as well
 as for practical applications, such as manipulation of soil microbiomes to
 manage agricultural pests and diseases.
description: This dataset was collected during a growth chamber experiment
 (2019), in which oak seedlings were growing with different natural soil
 communities, and exposed to (combinations of) different types of attackers
 (including aphids, powdery mildew and chewing caterpillars). Data was
 collected on seedling development (height, size of largest leaf, number of
 leaves and number of shoots) and attacker performance (aphid population
 size and mildew infection severity).
DOI: 10.5061/dryad.fj6q573sj
title: Gene expression dynamics during rapid organismal diversification of African cichlid fishes

description: Changes in gene expression play a fundamental role in phenotypic
 evolution. Transcriptome evolutionary dynamics have so far mainly been
 compared among distantly related species and remain largely unexplored
 during rapid organismal diversification, in which gene regulatory changes
 have been suggested as particularly effective drivers of phenotypic
 divergence. Here, we studied gene expression evolution in a model system
 of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By
 comparing gene expression profiles of six different organs in 74 cichlid
 species representing all subclades of this radiation, we demonstrate that
 the rate of gene expression evolution varies among organs, transcriptome
 parts, and the subclades of the radiation, indicating different strengths
 of selection. We found that the non-coding part of the transcriptome
 evolved more rapidly than the coding part, and that the gonadal
 transcriptomes evolved more rapidly than the somatic ones, with the
 exception of liver. We further show that the rate of gene-expression
 change was not constant over the course of the radiation but accelerated
 at its later phase. Finally, we show that – at the per-gene level – the
 evolution of expression patterns is dominated by stabilizing selection.
DOI: 10.5061/dryad.vq83bk3r1
title: Spatial scaling properties of coral reef benthic communities

description: The spatial structure of ecological communities on tropical coral reefs
 across seascapes and geographies have historically been poorly understood.
 Here we addressed this for the first time using spatially expansive and
 thematically resolved benthic community data collected around five
 uninhabited central Pacific oceanic islands, spanning 6° latitude and 17°
 longitude. Using towed-diver digital image surveys over ~140 linear km of
 shallow (8 – 20 m depth) tropical reef, we highlight the autocorrelated
 nature of coral reef seascapes. Benthic functional groups and hard coral
 morphologies displayed significant spatial clustering (positive
 autocorrelation) up to kilometre-scales around all islands, in some
 instances dominating entire sections of coastline. The scale and strength
 of these autocorrelation patterns showed differences across geographies,
 but patterns were more similar between islands in closer proximity and of
 a similar size. For example, crustose coralline algae (CCA) were clustered
 up to scales of 0.3 km at neighbouring Howland and Baker Islands and
 macroalgae were spatially clustered at scales up to ~3 km at both
 neighbouring Kingman Reef and Palmyra Atoll. Of all the functional groups,
 macroalgae had the highest levels of spatial clustering across geographies
 at the finest resolution of our data (100 m). There were several cases
 where the upper scale at which benthic community members showed evidence
 of spatial clustering correlated highly with the upper scales at which
 concurrent gradients in physical environmental drivers were spatially
 clustered. These correlations were stronger for surface wave energy than
 subsurface temperature (regardless of benthic group) and turf algae and
 CCA had the closest alignments in scale with wave energy across functional
 groups and geographies. Our findings suggest such physical drivers not
 only limit or promote the abundance of various benthic competitors on
 coral reefs, but also play a key role in governing their spatial scaling
 properties across seascapes.
description: These files contain the percentage cover values of coral reef
 benthic organisms by 100m wide grids that encircle remote pacfic islands
 (Howland, Baker, Jarvis, Kingman and Palmyra).
 variable/CoralNet.code/FunctionalGroup/CoralNet.name/Genus/Morphology/Calcifier : are column headings that describe the identified benthic organism in terms of its genus, morphology and benthic category. Morphology_grouping _.2 : is the column with groupings used to classify the morphology of different corals for this study.  GRID_ID : Is the number of the grid cell that the benthic data are located within. The grid cells were overlaid on top of the spatial benthic data using ArcMap software. Avg_LAT/Avg_LON : is the average lattitude and longitude of the photos contained within each grid cell Count_ : is the number of photos contained within each grid cell
DOI: 10.5061/dryad.5hqbzkh49
title: Thermal effects vary predictably across levels of organization: empirical results and theoretical basis

description: Thermal performance curves have provided a common framework to study the
 impact of temperature in biological systems. However, few generalities
 have emerged to date. Here we combine an experimental approach with
 theoretical analyses to demonstrate that performance curves are expected
 to vary predictably with the levels of biological organization. We
 measured rates of enzymatic reactions, organismal performance and
 population viability in Drosophila acclimated to different thermal
 conditions and show that performance curves become narrower with thermal
 optima shifting towards lower temperatures at higher levels or
 organization. We then explain these results on theoretical grounds,
 showing that this pattern reflects the cumulative impact of asymmetric
 thermal effects that piles up with complexity. These results and the
 proposed framework are important to understand how organisms, populations
 and ecological communities might respond to changing thermal conditions.
description: Outbred Drosophila stocks were maintained for five generations in
 the laboratory, and flies from these stocks were then separated into four
 different temperature acclimation treatments. Individuals were randomly
 sampled and employed in measurements of hexokinase specific enzymatic
 activity, whole-organismal metabolic rate, maximum running speed and
 viability. All measurements encompass males and females from the same
 generation, and specific details regarding the procedures to estimate
 these variables are available in the original paper.  
description: Please see Readme.txt for additional details.
DOI: 10.5061/dryad.3j9kd51gc
title: The Colorado River Delta and California’s Central Valley are critical regions for many migrating North American landbirds

description: Migration is an important component of some species full annual cycle.
 California’s Central Valley and the Colorado River Delta provide important
 riparian and wetland habitats for migrating waterbirds in the arid west of
 North America, but little is known about whether these locations are
 important at the population level to migrating landbirds. We used eBird
 Status and Trends abundance data to quantify the importance of the Central
 Valley and Colorado River Delta to landbirds by estimating the proportion
 of the breeding population of 112 species that use each site during
 migration. We found that ~17 million landbirds use the Colorado River
 Delta in the spring and ~14 million in the fall. Across four study regions
 in the Central Valley, up to ~65 million landbirds migrate through in the
 spring and up to ~48 million in the fall. In the spring and fall,
 respectively, up to 37 and up to 30 species had at least 1% of their
 continental population migrate through the study regions. We also
 quantified the spatial concentration of each species across latitudinal
 transects to determine the extent to which study regions were acting as
 migratory bottlenecks.  Landbird abundances were spatially
 concentrated in study regions 29.4% of all migration weeks, indicating
 that each study region acts as a migratory bottleneck. This application of
 eBird data is a powerful approach to quantifying the importance of sites
 to migrating birds. Our results provide evidence of population-level
 importance of the Central Valley and Colorado River Delta for many
 migratory landbirds.
description: See README file.
description: Figures S3 and S4
DOI: 10.5061/dryad.j3tx95xc1
title: Parallelism in endocarp form sheds light on fruit syndrome evolution in Viburnum

description: All Viburnum species produce drupes with a hardened endocarp surrounding a
 single seed. Endocarp form varies greatly within Viburnum, and differences
 in shape have long been used to distinguish major subclades. Here we trace
 the evolution of Viburnum endocarp shape using morphometric analyses and
 phylogenies for 115 Viburnum species. Endocarp measurements were obtained
 from fruits sampled from herbarium specimens and from field collections,
 and shapes were analyzed using elliptical Fourier analysis. We infer that
 the first viburnums had flattened and grooved endocarps. Subsequently,
 there were multiple losses of grooving in conjunction with shifts to both
 highly flattened and nearly round endocarps. In several clades the
 parallel evolution of a derived endocarp shape was accompanied by changes
 in a suite of other fruit traits, yielding distinctive fruit syndromes
 likely related to bird dispersal. However, in other clades endocarp shapes
 similar to the ancestral form have been retained while other fruit traits
 (color, amount of flesh, nutritional content) have diverged. We quantify
 cases of parallel evolution in endocarp shape that cut across recognized
 fruit syndromes such as red, carbohydrate rich fruits with flattened
 endocarps or blue, lipid rich fruits with round endocarps. Our analyses
 now invite studies of function and the selective factors that have yielded
 the distinctive suites of fruit and seed traits that distinguish the major
 Viburnum lineages.
description: Sequence data were collected for 10 gene regions, nine plastid
 regions (matK, ndhF, petB-petD, psbA-trnH, rbcL, rpl32-trnL, trnC-ycf6,
 trnK, trnS-trnG) and the nuclear ribosomal intergenic spacer region (ITS).
 Sequences were aligned using MUSCLE v 3.8.31, and subjected to
 phylogenetic analysis under maximum likelihood using Garli v 2.0 and using
 Bayesian Inference using MrBayes v 3.2.6. Morphological
 data were collected from digitized images of seed cross sections or
 digitized Camera Lucida drawings. Measurements included seed length,
 width, and height. Height was measured as perceived and actual height of
 the seed. Volume was calculated using the equation for the volume of an
 ellipsoid (4/3πabc) with the length (a), width (b), and perceived height
 (c) measurements.
DOI: 10.5061/dryad.x95x69pgg
title: Cross-sectional and prospective data on Framingham risk score, allostatic load, and ankle brachial index among Puerto Rican adults from the Boston Puerto Rican Health Study

description: Background Puerto Ricans have higher odds of peripheral artery disease
 (PAD) compared with Mexican Americans. Limited studies have examined
 relationships between clinical risk assessment scores with PAD
 assessments. Methods Using 2004-2015 data from the Boston Puerto Rican
 Health Study (BPRHS) (n = 370-583), cross-sectional, 5-y change and
 patterns of change in Framingham Risk Score (FRS) and allostatic load (AL)
 with ankle brachial index (ABI) at 5-y follow-up was assessed among Puerto
 Rican adults (45-75 y). Analysis were conducted in 2020. FRS and AL were
 calculated at baseline, 2-y and 5-y follow-up. Multivariable linear
 regression models examined cross-sectional and 5-y changes in FRS and AL
 with ABI at 5-y. Latent growth mixture modeling identified trajectories of
 FRS and AL over 5-y, and multivariable linear regression models were used
 to test associations between trajectory groups at 5-y. Results Greater FRS
 at 5-y and increases in FRS from baseline were associated with lower ABI
 at 5-y (β = -0.149, p = 0.010; β = -0.171, p = 0.038, respectively). AL
 was not associated with ABI in cross-sectional or change analyses.
 Participants in low-ascending (vs. no change) FRS trajectory, and
 participants in moderate-ascending (vs. low-ascending) AL trajectory, had
 lower 5-y ABI (β = -0.025, p = 0.044; β = -0.016, p = 0.023,
 respectively). Conclusions FRS was a better overall predictor of ABI,
 compared with AL. FRS may be a clinically feasible measure of PAD risk in
 Puerto Ricans, an understudied population. Additional research examining
 relationships between FRS and AL and development of PAD is warranted.
description: Please read the READ ME.txt: There are six
 data sets were used in this analysis, please use the data structure and
 dictionary workbook as a guide to target the corresponding datasets and
 models/Usage. You can find following information of a
 data set in the metadata workbook: name, Usage, size, observations, number
 of variables, and variable list, which contains variable name and lable,
 and identifier tag(yes/no). Due to only on more then
 three identifiers are allowed to be included in one data set. We removed
 Height(cn), Weight(kg), Body mass index (kg/m2), and Waist
 circumference(cm) from the original data set abi_table1. This action
 doesn't affect the analysis, since these variable weren't used
 in any of the models.
DOI: 10.5061/dryad.h44j0zphq
title: Carpophiline-ID: An interactive matrix-based key to the carpophiline sap beetles (Coleoptera, Nitidulidae) of Eastern North America

description: We present Carpophiline-ID, a matrix-based LucidTM key, for the adult
 stage of the known species of Carpophilinae (Coleoptera: Nitidulidae) of
 North America, east of the Mississippi River. We provide an overview of
 the features and technical specifications used to build the key. The list
 of terminal taxa used in the key represents the most current regional
 account for Carpophilinae, a beetle subfamily of agricultural and
 ecological importance. We discuss the value of matrix-based, free access
 keys for the identification of difficult taxa.
description: This dataset was developed to form the basis of a
 Lucid<sup>TM</sup> interactive key. Derived from original
 observations of the specimens as well as from taxonomic
 literature.
description: This dataset is formatted for use in
 the Lucid<sup>TM</sup> key platform. The ReadMe file describes
 the files contained in the zipped CarpophilineID folder and how to use
 them.
DOI: 10.5061/dryad.0cfxpnw0d
title: Data from: Corrigendum to: Deep learning improves taphonomic resolution: high accuracy in differentiating tooth marks made by lions and jaguars

description: Corrigendum to "Deep learning improves taphonomic resolution: high
 accuracy in differentiating tooth marks made by lions and jaguars".
 In a previous paper, we presented some convolutional neural network (CNN)
 models to classify images of tooth scores made by lions and jaguars
 through deep learning computer vision. In that work, we reached an
 accuracy of 82% of the testing set correctly classified. However, such an
 accuracy is biased, since the original sample was highly unbalanced.
 Therefor, now we present the results which correct the problems of the
 previously published models by producing more balanced classifications and
 also by achieving higher accuracy.
description: Images (.bpm) corresponding to lion and jaguar tooth scores,
 captured using Optika (30x) and resized and converted to grayscales to
 avoid bias.  Artificial intelligence models: VGG19,
 Densenet 201, ResNet50, Inception V3 and InceptionResNetV2.
description: Programming language: Python. The architectures were trained on
 70% of the original image set. The resulting models were subsequently
 tested against the 30% remaining sample, which was not used during the
 training. Training was performed through mini-batch kernels (size = 32).
 Testing was made using mini-batch kernels of size 20. Weight update was
 made using a backpropagation process for 100 epochs.