cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7sg523n
title: Data from: Indirect legacy effects of an extreme climactic event on a marine megafaunal community

description: While extreme climactic events (ECEs) are predicted to become more
 frequent, reliably predicting their impacts on consumers remains
 challenging– particularly for large consumers in marine environments. Many
 studies that do evaluate ECE effects focus primarily on direct effects,
 though indirect effects can be equally or more important. Here, we
 investigate the indirect impacts of the 2011 “Ningaloo Niño” marine
 heatwave ECE on a diverse megafauna community in Shark Bay, Western
 Australia. We use an 18 year community level dataset before (1998-2010)
 and after (2012-2015) the heatwave to assess the effects of seagrass loss
 on the abundance of seven consumer groups: sharks, sea snakes (multiple
 species), Indo-pacific bottlenose dolphins (Tursiops aduncus), dugongs
 (Dugong dugon), green turtles (Chelonia mydas), loggerhead turtles
 (Caretta caretta), and pied cormorants (Phalacrocorax spp.). We then
 assess whether seagrass loss influences patterns of habitat use by the
 latter five groups, which are under risk of shark predation. Sharks catch
 rates were dominated by the generalist tiger shark (Galeocerdo cuvier) and
 changed little, resulting in constant apex predator density despite heavy
 seagrass degradation. Abundances of most other consumers declined markedly
 as food and refuge resources vanished, with the exception of generalist
 loggerhead turtles. Several consumer groups significantly modified their
 habitat use patterns in response to the die-off, but only bottlenose
 dolphins did so in a manner suggestive of a change in risk-taking
 behavior. We show that ECEs can have strong indirect effects on megafauna
 populations and habitat use patterns in the marine environment, even when
 direct effects are minimal. Our results also show that indirect impacts
 are not uniform across taxa or trophic levels and suggest that generalist
 marine consumers are less susceptible to indirect effects of ECEs than
 specialists. Such non-uniform changes in populations and habitat use
 patterns have implications for community dynamics, such as the relative
 strength of direct predation and predation risk. Attempts to predict
 ecological impacts of ECEs should recognize that direct and indirect
 effects often operate through different pathways and that taxa can be
 strongly impacted by one even if resilient to the other.
description: Nowicki_Transect_Raw_Data_2-19-2019Transect Data (over 27,000 animals over more than 14,000 km of transect surveys over 17 years) used for all transect analyses and for creation of Figure 4. File includes Standardized Data, a Column Key, and a Readme tab.
DOI: 10.34894/s1bihj
title: Early Modern Dutch Colonial Court Records, 1637-1828

description: &lt;p&gt;
The dataset &lt;b&gt;Early Modern Dutch Colonial Court Records, 1637-1828&lt;/b&gt; was created as part of the project &lt;i&gt;Resilient Diversity: the Governance of Racial and Religious Plurality in the Dutch Empire, 1600-1800&lt;/i&gt;, coordinated by Catia Antunes, Ulbe Bosma, Karwan Fatah-Black and Matthias van Rossum, and hosted at the Leiden University and International Institute of Social History (2017-2022).
&lt;/p&gt;
&lt;p&gt;
Contributors to the dataset are: Imran Canfijn, Alexander Geelen, Elisabeth Heijmans, Bram van den Hout, Ramona Negrón, Bas Rensen, Sophie Rose, Matthias van Rossum, Rafaël Thiebaut, Merve Tosun, Hanna te Velde (v1.0 and v1.2.2), and Stefan Reyes (v1.2.2).
&lt;/p&gt;
&lt;p&gt;
&lt;b&gt;Created:&lt;/b&gt; 2016-2020&lt;br&gt;
&lt;b&gt;Version:&lt;/b&gt; 1.0 (2020); 1.2.2 (2025)&lt;br&gt;
&lt;b&gt;Sources:&lt;/b&gt; Nationaal Archief (The Hague), 1.04.02; 1.04.18.03; 1.05.03; 1.05.14; 1.05.01.02; 1.05.10.02; 1.11.06.08; 1.11.06.11; 3.03.02.
&lt;/p&gt;
DOI: 10.5061/dryad.c797f04
title: Data from: Genetic relatedness delineates the social structure of southern Australian bottlenose dolphins

description: Social relationships represent an adaptive behavioural strategy that can
 provide fitness benefits to individuals. Within mammalian societies,
 delphinids are known to form diverse grouping patterns and show a variety
 of social systems. However, how ecological and intrinsic factors have
 shaped the evolution of such diverse societies is still not well
 understood. In this study we used photo-identification data and biopsy
 samples collected between March 2013 and October 2015 in Coffin Bay, a
 heterogeneous environment in South Australia, to investigate the social
 structure of southern Australian bottlenose dolphins (Tursiops cf.
 australis). Based on data from 657 groups of dolphins we used generalized
 affiliation indices, and applied social network and modularity methods to
 study affiliation patterns among individuals and investigate the potential
 presence of social communities within the population. In addition, we
 investigated genetic relatedness and kinship relationships within and
 between the communities identified. Modularity analysis revealed that the
 Coffin Bay population is structured into two similar sized, mixed-sex
 communities which differed in ranging patterns, affiliation levels and
 network metrics. Lagged association rates also indicated that non-random
 affiliations persisted over the study period. The genetic analyses
 suggested that there was higher relatedness, and a higher proportion of
 inferred full-sibs and half-sibs, within than between communities. We
 propose that differences in environmental conditions between the bays and
 kinship relationships are important factors contributing to the
 delineation and maintenance of this social structure.
description: Database IDs_Sex_Group
 size_Locations_Behaviour_MicrosatsData collected in the
 field (Coffin Bay, South Australia).The first spreadsheet contains all the
 information associated with the photo-Id database (including locations,
 group size, date, behaviour and communities assigned). The second
 spreadsheet contains the allele size for the loci used in this study and
 the respective IDs. All details are provided in the first row of each
 spreadsheet.Database ID_Sex_Group
 size_locations_Behaviour_Microsats.xlsx
DOI: 10.5061/dryad.6g0p74j
title: Data from: The costs and benefits of multicellular group formation in algae

description: The first step in the evolution of complex multicellular organisms
 involves single cells forming a cooperative group. Consequently, to
 understand multicellularity, we need to understand the costs and benefits
 associated with multicellular group formation. We found that in the
 facultatively multicellular algae Chlorella sorokiniana: (1) the presence
 of the flagellate Ochromonas danica or the crustacean Daphnia magna leads
 to the formation of multicellular groups; (2) the formation of
 multicellular groups reduces predation by O. danica, but not by the larger
 predator D. magna; (3) under conditions of relatively low light intensity,
 where competition for light is greater, multicellular groups grow slower
 than single cells; (4) in the absence of live predators, the proportion of
 cells in multicellular groups decreases at a rate that does not vary with
 light intensity. These results can explain why, in cases such as this
 algae species, multicellular group formation is facultative, in response
 to the presence of predators.
description: Data
DOI: 10.34894/v7izi0
title: VOC Court Records Cape Town, 1705-1774

description: The dataset ‘VOC Court Records Cape Town, 1705-1774' was created as part of the project 'Resilient Diversity: the Governance of Racial and Religious Plurality in the Dutch Empire, 1600-1800', coordinated by Catia Antunes, Ulbe Bosma, Karwan Fatah-Black and Matthias van Rossum, and hosted at the Leiden University and International Institute of Social History (2017-2022). Sources: Nationaal Archief (The Hague), 1.04.02
DOI: 10.5061/dryad.6s82f20
title: Data from: Evidence of high genetic diversity and significant population structuring in Vachellia tortilis (Forsk.) Galasso & Bonfi population in Kenya

description: Context: Vachellia tortilis is an important dryland tree species valued
 for fuelwood and fodder production, however, no strategy has been put in
 place for sustainable management of the species genetic resources.
 Furthermore, there is inadequate information on the species population
 genetics to facilitate development of such strategies. Aim: We evaluated
 the amount and structure of neutral genetic diversity of V. tortilis
 population in Kenya and provided recommendations necessary for improvement
 and conservation of the species genetic resources. We hypothesised that
 the current genetic diversity of V. tortilis is high because of it is
 demographic history and that no population structuring was expected to
 occur due to the presumed long distance and effective gene flow within the
 species. Methods: Leaf tissues were collected from fifteen putative
 natural populations of V. tortilis covering the whole distribution range
 in Kenya. DNA was isolated from the leaf tissues and analysed using
 microsatellite markers. In total, 450 trees were genotyped using 10
 polymorphic nuclear microsatellite loci, and genetic diversity and
 population structure parameters determined Results: We found high levels
 of genetic diversity within the populations with a mean gene diversity at
 0.85. However, significant population differentiation was evident (FST =
 0.026, P = 0.007; RST = 0.032, P = 0.004) despite large number of migrants
 per generation (Nm = 5.3). Population structure detected suggests presence
 of two clusters, although, some populations showed mixed ancestry. The
 groups reflect the influence of geographic patterns and historical
 population gene flow. Conclusion: There exist high genetic diversity in V.
 tortilis in Kenya with significant population structuring into two
 clusters. We recommend consideration of the two distinct groups in the
 development of the species improvement, breeding and conservation
 programmes. Such programmes should ensure maintenance of the majority of
 the extant genetic diversity.
description: Microsatellite genotype
 data of 15 populations of Vachelia tortilis in KenyaThe data was generated
 by genotyping 15 populations of Vachellia tortilis in Kenya using 10
 microsatellite markers. 30 individual trees were randomly sampled per
 population, giving a total of 450 samples. Each locus is represented by
 two alleles called based on the allele size. Missing data is represented
 by zero (0)
DOI: 10.5061/dryad.2mj7019
title: Data from: Selection on structural allelic variation biases plasticity estimates

description: Wang and Althoff (2019) explored the capacity of Drosophila melanogaster
 to exhibit adaptive plasticity in a novel environment. In a full-sib,
 half-sib design, they scored the activity of the enzyme alcohol
 dehydrogenase (ADH) and plastic responses, measured as changes in ADH
 activity across ethanol concentrations in the range of 0-10% (natural
 variation) and 16% (the novel environment). ADH activity increased with
 alcohol concentration, and there was a positive association between larval
 viability and ADH activity in the novel environment. They also reported
 that families exhibiting greater plasticity had higher larval survival in
 the novel environment, concluding that ADH plasticity is adaptive.
 However, the four authors now concur that, since the study estimated
 plasticity from phenotypic differences across environments using full-sib
 families, it is not possible to disentangle the contributions of allele
 frequency changes at the Adh locus from regulatory control at loci known
 to influence ADH activity. Selective changes in allele frequencies may
 thus conflate estimates of plasticity; any type of “plasticity” (adaptive,
 neutral, or maladaptive) could be inferred depending on allele
 frequencies. The problem of scoring sib-groups after selection should be
 considered in any plasticity study that cannot use replicated genotypes.
 Researchers should monitor changes in allele frequencies as one mechanism
 to deal with this issue.
description: SupportingInformationMATLAB code “ADH_plasticity.m”
DOI: 10.5061/dryad.tk47202
title: Data from: Resilin in the flight apparatus of Odonata (Insecta) – cap tendons and their biomechanical importance for the flight

description: In Odonata, a direct flight mechanism with specialised tendons evolved.
 One particular adaptation, the implementation of the rubber-like protein
 resilin in these cap tendons might be of major importance. Although,
 resilin was firstly described in one tendon of Odonata, no comprehensive
 study about the presence of resilin in the thorax exists yet. We
 investigated various species of Odonata, using µCT, dissection and
 fluorescence microscopy. Here we show a complete mapping of the odonatan
 pterothorax, regarding the presence of tendons and their properties. Thus,
 20-21 cap tendons in the pterothorax of Odonata show the presence of
 resilin. While performing outstanding and often aggressive flight
 manoeuvres, resilin can provide shock absorption against mechanical damage
 from strong impacts. It may further improve the wear and fatigue
 resistance due to resilin’s damping behaviour. Additionally, resilin in
 tendons can absorb and return kinetic energy to restore muscles to their
 original shape after contracting and help maintaining self-oscillation of
 the flight muscles. Here the material distribution within the direct
 flight system of Odonata and the biomechanical importance and possible
 function of resilin is discussed. These results are an important step
 towards the understanding of the complex form-material-function interplay
 of the insect cuticle.
description: MicroCT Raw
 DataµCT Data Set for
 Sympetrum striolatum including labels dataResilin
 PicturesAll fFluorescence
 microscopy pictures done for all investigated species
DOI: 10.5061/dryad.jk673fq
title: Data from: Bimodal pollination systems in Andean Melastomataceae involving birds, bats and rodents

description: Floral adaptation to a single most effective functional pollinator group
 leads to specialized pollination syndromes. However, adaptations allowing
 for pollination by two functional groups (bimodal pollination systems)
 remain a conundrum rarely investigated. We tested if floral scent and
 nectar traits of species visited by two functional pollinator groups
 indicate specialization on either one of the two or (intermediate) bimodal
 systems. We studied pollination biology in four species of Meriania
 (Melastomataceae) in the Ecuadorian Andes. Pollinator observations and
 exclusion experiments showed that each species was effectively pollinated
 by two functional groups (hummingbirds/bats; hummingbirds/rodents;
 flowerpiercers/rodents), nectar composition followed known bird
 preferences and scent profiles gave mixed support for specialization on
 bats and rodents. Our results suggest that nectar rewarding Meriania
 species have evolved stable bimodal pollination strategies with parallel
 adaptations to two functional pollinator groups. The discovery of rodent
 pollination is particularly important given its rarity outside of South
 Africa.
description: forDryaddata on stigmatic pollen loads, nectar volume, nectar sugar concentration, nectar sugars and floral scents of four Meriania species
DOI: 10.5061/dryad.jc7s27r
title: Data from: Urbanization drives unique latitudinal patterns of insect herbivory and tree condition

description: Urban landscapes are characterized by high proportions of impervious
 surface resulting in higher temperatures than adjacent natural landscapes.
 In some cities, like those at cooler latitudes, trees may benefit from
 warmer urban temperatures, but trees in many cities are beset with
 problems like drought stress and increased herbivory. What drives patterns
 of urban tree health across urbanization and latitudinal temperature
 gradients? In natural systems, latitude-herbivory relationships are
 well-studied, and recent temperate studies have shown that herbivory
 generally increases with decreasing latitudes (warmer temperatures).
 However, the applicability of this latitude-herbivory theory in
 already-warmed urban systems is unknown. In this study, we investigated
 how the interaction of urbanization, latitudinal warming, and scale insect
 abundance affected urban tree health. We predicted that trees in warmer,
 lower latitude cities would be in poorer health at lower levels of
 urbanization than trees at cooler, higher latitudes due to the interaction
 of urbanization, latitudinal temperature, and herbivory. To evaluate our
 predictions, we surveyed the abundance of scale insect herbivores on a
 single, common tree species (Acer rubrum) in eight US cities spanning 10°
 of latitude. We estimated urbanization at two extents, a local one that
 accounted for the direct effects on an individual tree, and a larger one
 that captured the surrounding urban landscape. We found that urban tree
 health did not vary with latitudinal temperature but was best predicted by
 local urbanization and herbivore abundance. We did not observe increased
 herbivore abundance in warmer, lower latitudes cities, but instead
 herbivore abundance peaked in the mid latitudes of our study. This study
 demonstrates that urban landscapes may deviate from classical theory
 developed in natural systems and reinforces the need for research
 reconciling ecological patterns in urban landscapes.
description: Scale insect abundance,
 impervious surface proportions, and temperature data for Acer rubrum study
 treesScale insect abundance,
 impervious surface proportions, and temperature data for Acer rubrum study
 trees. Scale insect abundance, tree condition, DBH, and Impervious surface
 (20 m) collected in the field. Impervious surface (125 m) and temperature
 data was sourced from GIS files and analyzed in R.DRYAD_OIKOS.xlsx
DOI: 10.5285/0aa0e3e8-d668-4dd4-9089-7bd0ede798d7
title: Dental Microwear Texture Analysis (DMTA) of tooth surfaces of fossil wolves from Britain and modern wolves from Poland version 2

description: Two Excel workbooks reporting dental microwear texture analysis (DMTA) raw data. These are values from scale-sensitive fractal analysis (SSFA), and areal surface texture analysis (based on a suite of parameters, most of which are defined by ISO-25718-2) for dental microwear texture analysis of tooth surfaces of wolves from Britain (MIS Se & MIS 7 a-c) and modern Poland wolves. This study examines the dietary adaptability of European grey wolves using dental microwear texture analysis (DMTA). These datasets offer new insights into the palaeoclimatic and palaeoenvironmental conditions under which grey wolves endured climate change in the past, free of anthropogenic influence. They further allow the identification of hitherto-hidden ecological stress today, thereby highlighting potential vulnerabilities in modern populations under current and future climate change.

Tooth surface casts were produced using high-resolution, which is optimised for imaging purposes. Epoxy tooth replicas were scanned with a Sensofar S neox.
MountainsMap Imaging Topography was utilised to quantify dental microwear texture parameters from Sensofar scans.
DOI: 10.5061/dryad.gh41n3j
title: Data from: Relationships between plant traits, soil properties and carbon fluxes differ between monocultures and mixed communities in temperate grassland

description: 1. The use of plant traits to predict ecosystem functions has been gaining
 growing attention. Aboveground plant traits, such as leaf nitrogen (N)
 content and specific leaf area (SLA), have been shown to strongly relate
 to ecosystem productivity, respiration, and nutrient cycling. Further,
 increasing plant functional trait diversity has been suggested as a
 possible mechanism to increase ecosystem carbon (C) storage. However, it
 is uncertain whether belowground plant traits can be predicted by
 aboveground traits, and if both above- and belowground traits can be used
 to predict soil properties and ecosystem-level functions. 2. Here, we used
 two adjacent field experiments in temperate grassland to investigate if
 above- and belowground plant traits are related, and whether relationships
 between plant traits, soil properties and ecosystem C fluxes (i.e.,
 ecosystem respiration and net ecosystem exchange) measured in potted
 monocultures could be detected in mixed field communities. 3. We found
 that certain shoot traits (e.g., shoot N and C, and leaf dry matter
 content) were related to root traits (e.g., root N, root C:N, and root dry
 matter content) in monocultures, but such relationships were either weak
 or not detected in mixed communities. Some relationships between plant
 traits (i.e., shoot N, root N and/or shoot C:N) and soil properties (i.e.,
 inorganic N availability and microbial community structure) were similar
 in monocultures and mixed communities, but they were more strongly linked
 to shoot traits in monocultures and root traits in mixed communities.
 Structural equation modelling showed that above- and belowground traits
 and soil properties improved predictions of ecosystem C fluxes in
 monocultures, but not in mixed communities on the basis of
 community-weighted mean traits. 4. Synthesis: Our results from a single
 grassland habitat detected relationships in monocultures between above-
 and belowground plant traits, and between plant traits, soil properties
 and ecosystem C fluxes. However, these relationships were generally weaker
 or different in mixed communities. Our results demonstrate that while
 plant traits can be used to predict certain soil properties and ecosystem
 functions in monocultures, they are less effective for predicting how
 changes in plant species composition influence ecosystem functions in
 mixed communities.
description: CP_DataSS_dataSelside Vegetation Survey Gas RingsSelside Vegetation Survey Whole Plots
DOI: 10.5061/dryad.8575jr5
title: Data from: Unioverse: a phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida)

description: Freshwater mussels (order Unionoida) are a diverse radiation of parasitic
 bivalves that require temporary larval encystment on vertebrate hosts to
 complete metamorphosis to their free-living phase. The freshwater
 mussel-fish symbiosis represents a useful relationship for understanding
 eco-evolutionary dynamics in freshwater ecosystems but the practicality of
 this promising model system is undermined by the absence of a stable
 freshwater mussel phylogeny. Inadequate character sampling is the primary
 analytical impediment obfuscating a coherent phylogeny of freshwater
 mussels, specifically the lack of nuclear molecular markers appropriate
 for reconstructing supraspecific relationships and testing
 macroevolutionary hypotheses. The objective of this study is to develop a
 phylogenomic resource, specifically an anchored hybrid enrichment probe
 set, capable of capturing hundreds of molecular markers from taxa
 distributed across the entirety of freshwater mussel biodiversity. Our
 freshwater mussel specific anchored hybrid enrichment probe set, called
 Unioverse, successfully captures hundreds of nuclear protein-coding loci
 from all major lineages of the Unionoida and will facilitate more
 data-rich and taxonomically inclusive reconstructions of freshwater mussel
 evolution. We demonstrate the utility of this resource at three disparate
 evolutionary scales by estimating a backbone phylogeny of the Bivalvia
 with a focus on the order Unionoida, reconstructing the subfamily-level
 relationships of the Unionidae, and recovering the systematic position of
 the phylogenetically unstable genus Plectomerus.
description: Transcriptome_AssembliesTranscriptome assemblies of Contradens contradens (UF 507562) and Scabies phaselus (UF 507552).Unioverse_reference_probe_regionsZipped folder containing the Unioverse reference probe regions.Unioverse_probesUnioverse probe sequences.Pipeline_ResultsTranscriptome and AHE data making through the processing pipeline.SupermatricesNT_Supermatrix, AA_Supermatrix, and each of the percent variable site supermatrices.TreesAll of the phylogenetic trees relevant to this study.