cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vq83bk3v0
title: Mapping breeding bird species richness at management-relevant resolutions across the United States

description: Human activities alter ecosystems everywhere, causing rapid biodiversity
 loss and biotic homogenization. These losses necessitate coordinated
 conservation actions guided by biodiversity and species distribution
 spatial data that cover large areas yet have fine-enough resolution to be
 management-relevant (i.e., ≤ 5 km). However, most biodiversity products
 are too coarse for management or are only available for small areas.
 Furthermore, many maps generated for biodiversity assessment and
 conservation do not explicitly quantify the inherent tradeoff between
 resolution and accuracy when predicting biodiversity patterns. Our goals
 were to 1) generate predictive models of overall breeding bird species
 richness and species richness of different guilds based on nine functional
 or life history-based traits across the conterminous US at three
 resolutions (0.5, 2.5, and 5 km), and 2) quantify the tradeoff between
 resolution and accuracy, and hence relevance for management, of the
 resulting biodiversity maps. We summarized eighteen years of North
 American Breeding Bird Survey data (1992-2019) and modeled species
 richness using random forests, including 66 predictor variables
 (describing climate, vegetation, geomorphology, and anthropogenic
 conditions), 20 of which we newly derived. Among the three spatial
 resolutions, the percent variance explained ranged from 27% to 60% (median
 = 54%; mean = 57%) for overall species richness and 12% to 87% (median =
 61%; mean = 58%) for our different guilds. Overall species richness and
 guild-specific species richness were best explained at 5-km resolution
 using approximately 24 predictor variables based on percent variance
 explained, symmetric mean absolute percentage error, and root mean squared
 error values. However, our 2.5-km resolution maps were almost as accurate
 and provided more spatially detailed information, which is why we
 recommend them for most management applications. Our results represent the
 first consistent, occurrence-based, and nationwide maps of breeding bird
 richness with a thorough accuracy assessment that are also spatially
 detailed enough to inform local management decisions. More broadly, our
 findings highlight the importance of explicitly considering tradeoffs
 between resolution and accuracy to create management-relevant biodiversity
 products for large areas.
DOI: 10.5061/dryad.280gb5mrh
title: Host traits measurements after evolution with or without parasites during range expansions

description: Rapid evolutionary changes during range expansions can lead to the
 divergence between range core and front populations, with the emergence of
 dispersal syndromes. Besides intraspecific effects, range expansions may
 be impacted by interspecific interactions such as parasitism. Yet, despite
 the potentially large impact of parasites imposing additional selective
 pressures on the host, their role on range expansions remains largely
 unexplored. Here, we investigated whether parasites affect the evolution
 of host dispersal syndromes during spatial spread. Using populations of
 the ciliate Paramecium caudatum and its bacterial parasite Holospora
 undulata spreading in microcosm landscapes, we studied experimental range
 expansions under the presence or absence of the parasite. We found that
 range expansion and parasite treatments acted independently on the
 evolution of host dispersal syndromes. Front host populations showed
 different trait associations between swimming behaviour and population
 growth parameters than core populations, indicating divergent evolution.
 The presence of parasites reshaped these trait associations and divergence
 between front and core, with hosts exposed to the parasite exhibiting
 overall reduced dispersal, but increased resistance. Our work shows that
 host-parasite interactions during range expansions can shift the
 contenders to novel evolutionary trajectories and may influence the speed
 of the range expansion itself and of spreading epidemics.
description: Travelling with a parasite dataset. Complete matrix of the traits
 measured for the 4 evolutionary treatments.
DOI: 10.5281/zenodo.18398882
title: Experimental Dataset and Processing Program for Rigid Cylinder Fluid–Structure Interaction Experiments

description: This repository contains raw experimental data, processed datasets, and MATLAB processing scripts for self-excited vibration experiments of a rigid circular cylinder. The data support reproducible analysis of vortex-induced vibration phenomena.
DOI: 10.5281/zenodo.18398883
title: Experimental Dataset and Processing Program for Rigid Cylinder Fluid–Structure Interaction Experiments

description: This repository contains raw experimental data, processed datasets, and MATLAB processing scripts for self-excited vibration experiments of a rigid circular cylinder. The data support reproducible analysis of vortex-induced vibration phenomena.
DOI: 10.5061/dryad.1zcrjdftm
title: Chimpanzees as ecosystem service providers: Seed dispersal of an economically important plant resource

description: Vertebrate-mediated seed dispersal is vital to the maintenance of
 diversity in tropical ecosystems, and seed-dispersing animals are
 increasingly thought to provide ecosystem services by dispersing the seeds
 of plant species utilized by people. However, few studies have
 demonstrated a link between vertebrate frugivores and plants used by
 people, thus limiting the generalizability of the
 seed-disperser-as-ecosystem-service-provider concept. We examined the
 effectiveness of western chimpanzees (Pan troglodytes verus) as seed
 dispersers (i.e., their influence on seedling recruitment) of an
 economically important fruit resource, Saba senegalensis, at the site of
 Fongoli, a savanna-woodland environment in southeastern Senegal. The fruit
 from the Saba vine is commonly harvested from the wild by local people and
 is also an important food item for chimpanzees. We conducted germination
 experiments on gut-passed seeds alongside non-gut-passed seeds and
 analyzed the germination success of chimpanzee-dispersed seeds in situ. We
 also analyzed the effect of habitat type and canopy cover at each seed
 dispersal site to determine which sites are most suitable for Saba
 germination. Germination trials showed that chimpanzee gut passage and
 manual pulp removal increased the likelihood of germination over seeds
 left intact. Nearly a quarter of chimpanzee-dispersed seeds germinated in
 situ and Saba seeds were distributed non-randomly throughout Fongoli, with
 more dispersed seeds found in habitats most suitable for Saba germination.
 These results suggest that chimpanzees aid in the early stages of Saba
 recruitment and thus provide an ecosystem service via seed dispersal that
 may contribute to the well-being of local people.
description: See the ReadMe file for information about data and
 variabales.
DOI: 10.5061/dryad.b8gtht7f0
title: Dataset for: Guidelines for standardising the application of discriminant analysis of principal components to genotype data

description: Data and scripts required to replicate the analyses in Thia (2022)
 "Guidelines for standardising the application of discriminant
 analysis of principal components to genotype data" in Molecular
 Ecology. This study aimed to address methodological misunderstandings and
 misuse of the DAPC method in population genetics. The analyses are used to
 illustrate that for genotype data comprising k effective populations,
 there are only k−1 PC axes that describe populations structure,
 and that are biologically informative. These PC axes are the only suitable
 axes for modelling the among-population differences with a DA. Use of many
 more than k−1 PC axes leads to decreasing biological relevancy of the
 final DA solution, with implications for misinterpretations of population
 structure.
description: Metapopulations with different migrations rates and levels of
 genetic differentaition were simualted
 using <em>fastsimcoal </em>v2.7.  Simulated
 individuals were imported into R v4.1.2 for further downstream
 analysis.
description: See the README for details on setting up computing environment,
 the working directory, and executing scripts.
DOI: 10.5061/dryad.9ghx3ffk2
title: Oak galls exhibit ant-dispersal convergent with myrmecochorous seeds

description: Ants disperse oak galls of some cynipid wasp species similarly to how they
 disperse seeds with elaiosomes. We conducted choice assays in field and
 lab settings, with ant-dispersed seeds and wasp-induced galls found in ant
 nests and found that seed-dispersing ants retrieve these galls as they do
 myrmecochorous seeds. We also conducted manipulative experiments in which
 we removed the putative ant-attracting appendages (“kapéllos”) from galls
 and found ants are specifically attracted to kapéllos. Finally, we
 compared chemical composition and the histology of ant-attracting
 appendages on seeds and galls, and they both had similar fatty-acid
 compositions as well as morphology. We also observed seed-dispersing ants
 retrieve oak galls to their nests, and rodents and birds consuming oak
 galls that were not retrieved by ants. These results suggest convergence
 in ant-mediated dispersal between myrmecochorous seeds and oak galls.
 Based on our observations, a protective advantage for galls retrieved to
 ant nests seems a more likely benefit than dispersal distance, as also has
 been suggested for myrmecochorous seeds. These results require
 reconsideration of established ant-plant research assumptions as
 ant-mediated seed and gall dispersal appear strongly convergent and galls
 may be far more abundant in eastern North American deciduous forests than
 myrmecochorous seeds.
DOI: 10.5061/dryad.tht76hf15
title: Dead Again: Predictions of repeat tree die-off under hotter droughts confirm mortality thresholds for a dryland conifer species

description: Tree die-off, driven by extreme drought and exacerbated by a warming
 climate, is occurring rapidly across every wooded continent - threatening
 carbon sinks and other ecosystem services provided by forests and
 woodlands. Forecasting the spatial patterns of tree die-off in response to
 drought is a priority for the management and conservation of forested
 ecosystems under projected future hotter and drier climates. Several
 drought-related metrics have recently been proposed to predict the
 mortality threshold (i.e., tipping point) for Pinus edulis, a model tree
 species in many studies of drought-induced tree die-off. To improve future
 capacity to forecast tree mortality, we used a severe drought in 2018
 across the southwestern United States as a natural experiment. We compared
 the ability of published mortality thresholds derived from four drought
 metrics (the Forest Drought Severity Index, the Standardized Precipitation
 Evapotranspiration Index, and raw values of precipitation and vapor
 pressure deficit) to predict areas of P. edulis die-off following extreme
 drought. Using aerial detection surveys of tree mortality in combination
 with gridded climate data, we calculated the agreement between these four
 proposed thresholds and the presence and absence of regional-scale tree
 die-off. Overall, such thresholds tended to over predict the spatial
 extent of tree die-off across the landscape, yet some retain moderate
 skill in discriminating between areas that experienced and did not
 experience tree die-off. Area under the curve (AUC) of these thresholds
 ranged from 0.51 to 0.71, sensitivity (true-positive rate) ranged from
 0.54 to 0.86, and specificity (true-negative rates) ranged from 0.16 to
 0.73. We highlight that empirically derived climate thresholds may be a
 useful forecasting tool to identify vulnerable areas to drought induced
 die-off, allowing for targeted responses to future droughts and improved
 management of at-risk areas.
description: Data from USDA Aerial Detection Surveys (Region 2, 3, and 4) for
 2019 and PRISM Climate Data, processed in R using the raster
 package.
DOI: 10.5061/dryad.tdz08kq1r
title: Data from: T cell morphodynamics reveal periodic shape oscillations in 3D migration

description: Surface segmentation data of cytotoxic T cells migrating in 3D collagen
 matrices, imaged by lattice light-sheet microscopy and used for
 quantitative morphodynamic analysis in the manuscript: T Cell
 Morphodynamics Reveal Periodic Shape Oscillations in 3D Migration.
DOI: 10.5061/dryad.xsj3tx9h7
title: Short-finned pilot whales exhibit behavioral plasticity in foraging strategies mediated by their environment

description: Predators adapt their foraging behavior to exploit a variety of prey in a
 range of environments. Short-finned pilot whales are wide-ranging
 predators in tropical and sub-tropical oceans, but most previous studies
 of their foraging ecology have been conducted near oceanic islands. We
 deployed sound and movement recording tags on 43 short-finned pilot whales
 off Cape Hatteras, North Carolina, USA, to measure their foraging behavior
 in a continental shelf-break ecosystem and investigate how variation in
 the environment shapes their behavior. Overall, the foraging behavior of
 pilot whales off Cape Hatteras was similar to that of their counterparts
 from island-associated habitats. Off Cape Hatteras, pilot whales made
 foraging dives as deep as 1077 m (mean: 445 m), lasting up to 23 min
 (mean: 12.8 min), with sprints (pursuit at speeds over 3 m/s and up to 6.9
 m/s) in more than half of foraging dives. However, tagged whales off Cape
 Hatteras produced higher buzz rates (11.3 buzzes/dive), foraged more
 extensively in daytime hours, and engaged in more frequent benthic
 foraging than island-associated ecotypes. By parsing the echoic scene
 generated by the animal’s own echolocation clicks, we show that pilot
 whales off Cape Hatteras frequently exploit bathymetric features for
 foraging, with benthic dives resulting in higher prey capture attempts
 than pelagic dives. The ability of these predators to strategically adapt
 foraging strategies to local habitat features likely contributes to their
 ecological success and may allow them to adjust to shifts in prey
 distributions in a rapidly changing Anthropocene ocean.
DOI: 10.5061/dryad.rjdfn2zct
title: Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles

description: Cerambycinae is the second-largest subfamily of longhorn beetles in the
 Southern Hemisphere. The phylogeny of Cerambycinae is poorly known,
 resulting in a highly artificial tribal-level classification and a largely
 speculative evolutionary history. We reconstructed the phylogenetic
 relationships of Cerambycinae at the generic level using anchored hybrid
 enrichment data from hundreds of nuclear genes, with a primary focus on
 the extraordinarily diverse faunas of Australia and New Zealand. We also
 estimated divergence times by incorporating fossil calibrations in our
 analyses. We identified two main clades within Cerambycinae, which can
 also be separated morphologically by a distinct type of antennal foramen.
 We recovered a Late Jurassic origin of crown Cerambycinae. Dorcasominae,
 which was newly found to have representatives in Australia, was notably
 derived from within Cerambycinae. We recovered two independent origins of
 Australian Cerambycinae: one clade originated in the Early Cretaceous and
 is likely endemic to the Southern Hemisphere, while the other clade
 appears to have immigrated to Australia, perhaps from the Northern
 Hemisphere. Within the Australian lineages were multiple independent
 origins of New Zealand taxa, all of which are relative host-plant
 generalists. Tribal relationships and assignments are discussed and, based
 on our results, the following major nomenclatural acts were made:
 Dorcasominae Lacordaire, 1868, is downgraded to a tribe Dorcasomini of
 Cerambycinae Latreille, 1804; Neostenini Lacordaire, 1868 syn. nov. is
 treated as a junior synonym of Uracanthini Blanchard, 1851.
description: Our taxon sample was designed with a focus on the faunas of
 Australia and New Zealand. Ethanol-preserved specimens of Cerambycinae
 deposited in the Australian National Insect Collection (ANIC) and the New
 Zealand Arthropod Collection (NZAC) comprised most specimens
 studied. Genomic DNA was extracted from thoracic muscle, normalized to
 100–500 ng of DNA, and sheared to 300–500 bp in size. Hybrid enrichment
 was performed following the myBaits Hybridization Capture for Targeted NGS
 protocol (Arbor Biosciences); the AHE probes were designed for Coleoptera
 by Haddad et al. (2018).
DOI: 10.5061/dryad.h44j0zpn2
title: Soil carbon composition and persistence under various management practices on Mollisols

description: This dataset contains information of the manuscript entitled
 "Persistent soil carbon enhanced in Mollisols by well-managed
 grasslands but not annual grain or dairy forage cropping systems".
 Grasslands-derived Mollisols cover a large area globally and are usually
 under intensive agricultural production, which has liberated large amounts
 of carbon (C) into the atmosphere. Whether improved management practices
 such as no-till, diversified crop rotations, legumes and/or manure
 additions, or re-establishing perennial grasslands and integrating
 livestock can restore soil C on Mollisols is unclear. In this study, we
 utilized the Wisconsin Integrated Cropping Systems Trial (WICST), a
 long-term trial comparing conventional and alternative agricultural
 systems in the North Central USA, and studied soil C composition and
 persistence, and their relationships with soil microbial attributes after
 29 years of different agricultural management.  The soil C
 composition data include particulate organic matter (POM)-C, which is
 believed to be primarily plant-derived and unprocessed or partially
 processed by microbes, and mineral-associated organic matter (MAOM)-C,
 which is believed to be mostly microbial-derived and simple structured.
 These soil C fractions were obtained by physical fractionation (53
 µm). Diffuse reflectance infrared fourier
 transform spectroscopy (DRIFTS) was used to study the composition of MAOM
 (Aliphatic C vs. Aromatic C). Soil microbial attributes studied include
 soil microbial biomass C (by chloroform fumigation method), microbial
 C-use efficiency (CUE) (by 13C-tracing method), and microbial necromass
 (amino sugars biomarkers, including glucosamine, muramic
 acids, galactosamine, and mannosamine). Activities of oxidative
 enzymes were studied to assess the potential of soil organic matter
 oxidation under these different management regimes. These data suggested
 that on the Mollisols, only perennial pastures that were managed by
 rotational grazing could enhance soil (0-30 cm) carbon stock and
 persistence compared to the conventional continuous corn system that had
 annual tillage. No-till did not increase soil C stock or persistence,
 while including legumes/manure in crop rotations could enhance microbial C
 cycling, but could not enhance the stock of persistent MAOM-C.
DOI: 10.5061/dryad.fttdz08vb
title: Squamation and scale morphology at the root of jawed vertebrates

description: Placoderms, as the earliest branching jawed vertebrates, are crucial to
 understanding how the characters of crown gnathostomes comprising
 Chondrichthyes and Osteichthyes evolved from their stem relatives. Despite
 the growing knowledge of the anatomy and diversity of placoderms over the
 past decade, the dermal scales of placoderms are predominantly known from
 isolated material, either morphologically or histologically, resulting in
 their squamation being poorly understood. Here we provide a comprehensive
 description of the squamation and scale morphology of a primitive taxon of
 Antiarcha (a clade at the root of jawed vertebrates), Parayunnanolepis
 xitunensis, based on the virtual restoration of an articulated specimen by
 using X-ray computed tomography. Thirteen morphotypes of scales are
 classified to exhibit how the morphology changes with their position on
 the body in primitive antiarchs, based on which nine areas of the
 post-thoracic body are distinguished to show their scale variations in the
 dorsal, flank, ventral, and caudal lobe regions. In this study, the
 histological structure of yunnanolepidoid scales is described for the
 first time based on disarticulated scales from the type locality and
 horizon of P. xitunensis. The results demonstrate that yunnanolepidoid
 scales are remarkably different from their dermal plates as well as
 euantiarch scales in lack of a well-developed middle layer. Together, our
 study reveals that the high regionalization of squamation and the
 bipartite histological structure of scales might be plesiomorphic for
 antiarchs, and jawed vertebrates in general.
description: This study involves the holotype of <em>P</em>.
 <em>xitunensis</em> IVPP V11679.1 and six disarticulated
 scales IVPP V28642–V28647 from Xitun village, Cuifengshan in Qujing city
 (Yunnan Province). They were collected from the middle part of the Xitun
 Formation (late Lochkovian) and housed in the Institute of Vertebrate
 Paleontology and Paleoanthropology. V11679.1 was
 scanned using the Nano-CT system (Phoenix x-ray, GE Measurement &
 Control) at a pixel resolution of 5.99 μm in the Key Laboratory of
 Vertebrate Evolution and Human Origins of Chinese Academic of Science,
 Beijing. It was scanned at 90 kV, 100 μA, 1 s exposure time, with a 9 μm
 focal spot size. V28642–V28647 were processed with the diluted acetic acid
 and then scanned using the Nano-CT at 80 kV and100 μA, with a 1.85 μm
 voxel size. Raw data were pre-processed in VG Studio Max 3.3, and
 reconstructions were performed using Mimics 19.0.
description: CT scan data are available in Mimics, reconstructions (exported
 as .stl files) in VG Studio Max and scale measurement data in Microsoft
 Excel.
DOI: 10.15468/dl.2xt64k
title: Occurrence Download

description: A dataset containing 6590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Occurrence Data of Vascular Plants collected or compiled for the Flora of Bavaria",
 "Geometry POLYGON((9.88727 49.7514,9.97079 49.7514,9.97079 49.82416,9.88727 49.82416,9.88727 49.7514))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1500-2024"
 ]
}

 The dataset includes 6590 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003045-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.