cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7b423q5
title: Data from: Rapid Pliocene adaptive radiation of modern kangaroos

description: Differentiating between ancient and younger, more rapidly evolved clades
 is important for determining paleoenvironmental drivers of
 diversification. Australia possesses many aridity-adapted lineages, the
 origins of which have been closely linked to late Miocene continental
 aridification. Using dental macrowear and molar crown height measurements,
 spanning the past 25 million years, we show that the most iconic
 Australian terrestrial mammals, “true” kangaroos (Macropodini), adaptively
 radiated in response to mid-Pliocene grassland expansion rather than
 Miocene aridity. In contrast, low-crowned, short-faced kangaroos radiated
 into predominantly browsing niches as the late Cenozoic became more arid,
 contradicting the view that this was an interval of global browser
 decline. Our results implicate warm-to-cool climatic oscillations as a
 trigger for adaptive radiation and refute arguments attributing
 Pleistocene megafaunal extinction to aridity-forced dietary change.
description: Couzens&Prideaux_dryad_packCompressed directory containing data files (.csv,.txt) and R script files.Couzens&Prideaux2018_dryad_package.zipREAD_ME.txt
DOI: 10.5061/dryad.rj10fh0
title: Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

description: The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive
 radiation. However, like many island plant lineages, no fossils have been
 assigned to the clade. As a result, the clade's age and
 diversification rate are not known precisely, making it difficult to test
 biogeographic hypotheses about the radiation. Without fossils,
 paleogeographically structured biogeographic processes may inform species
 divergence times; for example, an island must first exist for a clade to
 radiate upon it. We date the silversword clade and test biogeographic
 hypotheses about its radiation across the Hawaiian Archipelago by modeling
 interactions between species relationships, molecular evolution,
 biogeographic scenarios, divergence times, and island origination times
 using the Bayesian phylogenetic framework, RevBayes. The ancestor of
 living silverswords most likely colonized the modern Hawaiian Islands once
 from the mainland approximately 5.1 Ma, with the most recent common
 ancestor of extant silversword lineages first appearing approximately 3.5
 Ma. Applying an event-based test of the progression rule of island
 biogeography, we found strong evidence that the dispersal process prefers
 old-to-young directionality, but strong evidence for diversification
 continuing unabated into later phases of island ontogeny, particularly for
 Kauai. This work serves as a general example for how diversification
 studies benefit from incorporating biogeographic and paleogeographic
 components.
description: Hawaiian silversword
 datasetThe zip file contains
 all input data for the silversword analysis: the ITS molecular alignment,
 taxon range data for the six discrete areas, the paleogeographic
 connectivity matrices, the times of island formation, and the
 area-distance matrix.landis_et_al_silversword_data.zipHawaiian silversword outputThis archive contains output used in the "Retracing the Hawaiian silversword radiation". Model settings correspond to the preferred diversification and taxon sampling settings, and for the three model types: full paleogeography (G4), hotspot-naive (G1), and geography-naive (G0). See main text for details.landis_et_al_silversword_output.zipHawaiian silversword radiation historiesThis archive contains figures of evolutionary histories for the silversword radiation. Each figure shows the dated tree, its topology, range evolution histories, and paleogeographic island ages. Only 100 of 1000 histories shown. Model settings correspond to the preferred diversification and taxon sampling settings, and for the three model types: full paleogeography (G4), hotspot-naive (G1), and geography-naive (G0). See main text for details.landis_et_al_silversword_radiation_histories.zip
DOI: 10.5061/dryad.1g511q5
title: Data from: An empirical and mechanistic explanation of abundance-occupancy relationships for a critically endangered nomadic migrant

description: The positive abundance-occupancy relationship (AOR) is a pervasive pattern
 in macroecology. Similarly, the association between occupancy (or
 probability of occurrence) and abundance is also usually assumed to be
 positive and in most cases constant. Examples of AORs for nomadic species
 with variable distributions are extremely rare. Here we examined temporal
 and spatial trends in the AOR over seven years for a critically endangered
 nomadic migrant which relies on dynamic pulses in food availability to
 breed. We predicted a negative temporal relationship, where local mean
 abundances increase when the number of occupied sites decreases, and a
 positive relationship between local abundances and the probability of
 occurrence. We also predicted that these patterns are largely attributable
 to spatiotemporal variation in food abundance. The temporal AOR was
 significantly negative and annual food availability was significantly
 positively correlated with the number of occupied sites, but negatively
 correlated with abundance. Thus, as food availability decreased, local
 densities of birds increased, and vice-versa. The abundance - probability
 of occurrence relationship was positive and non-linear, but varied between
 years due to differing degrees of spatial aggregation caused by changing
 food availability. Importantly, high abundance (or occupancy) did not
 necessarily equate to high quality habitat and may be indicative of
 resource bottlenecks or exposure to other processes affecting vital rates.
 Our results provide a rare empirical example that highlights the
 complexity of AORs for species that target aggregated food resources in
 dynamic environments.
description: 2009-2015_swift parrot
 data_abundance and occupancyThese data relates to
 the site based and landscape scale analyses in the study. One spreadsheet
 is identified as site based, another landscape scale
 based.2009-2015_abundance and
 occupancy_dryad.xlsx
DOI: 10.5061/dryad.233771m
title: Data from: Hyper-longirostry and kinematic disparity in extinct toothed whales

description: Toothed cetacean (Odontoceti) lineages in the Miocene and Pliocene evolved
 rostra that are proportionally more elongate than any other aquatic mammal
 or reptile, living or extinct. Their similarities in cranial proportions
 to billfish may suggest a convergent feeding style, where the rostrum is
 swept through the water to hit and stun prey. Here we calculated second
 moment of area from rostral cross-sections of these fossil odontocete
 taxa, as well as from extant ecological analogues, to infer variation in
 feeding behavior. Our results show that the extremely long rostra of
 extinct toothed whales vary considerably in functionally relevant measures
 of shape, and likely exhibited a diversity of feeding behaviors, ranging
 from those similar to modern odontocetes to those convergent with
 billfish. Eustatic sea-level and temperature maxima of the Miocene likely
 led to changes in prey characteristics or abundance that enabled the
 repeated evolution of this extreme morphotype, which later went extinct
 during late Pliocene climatic deterioration.
description: Supplementary Figure 1:
 Comparison between methodological approachesLog10 xx/zz values using
 two different approaches. A: analyses using the external morphology of the
 models and B: incorporating internal morphology.Supplementary Figure
 1.tifSupplementary Table 1:
 Rostral measurements taken from various taxa.Table of condylar basal
 length, rostral length and rostral index used to create Figure
 2.Supplementary Table
 1.xlsx
DOI: 10.5061/dryad.k0kj062
title: Data from: The association between method of solicitation and patient permissions for use of surplus tissues and contact for future research

description: Objective: Obtaining patient permissions for research contact and for
 surplus tissue use as part of routine clinical practice can improve
 research participation. This study aims to investigate the difference in
 patient permissions for use of surplus tissues, and for direct contact for
 research, using two different methods of solicitation. Methods: An opt-in,
 population-based approach for gathering research permissions was
 implemented in two methods. The first method, applied a 2 –item patient
 questionnaire delivered through the EHR patient portal. The questionnaire
 composed of two questions 1) whether de-identified surplus specimens may
 be used for research) and 2) whether patients could be contacted about
 research. In the second method, the same questionnaire was physically
 presented in clinic within the clinical workflow. We used 1 to 1
 propensity score matching and multivariate logistic regression to estimate
 the odds of obtaining permission and the difference between the two
 methods of solicitation. Results: The propensity score model matched 8044
 observations (4114 submissions in each group). Among the in-clinic
 submission group, 70.13% provided permission for surplus tissue compared
 to 66.65% in the patient portal submission group (OR=1.20; 95% CI
 1.09-1.32; p&lt;0.001). Permission for future research contact was
 similar among in-clinic (65.07%) and patient portal submission (66.65%)
 groups (OR=0.94; 95% CI 0.85-1.03; p=0.175). These trends were consistent
 among European Americans and African American patients. However, among
 patients of other race, higher permission for both future contact
 (OR=0.58; 95% CI 0.39-0.86; p&lt;0.007) and surplus tissue use
 (OR=0.65; 95% CI 0.43-0.97; p=0.036) was observed among patient portal
 submission.
description: manuscript_data
DOI: 10.5061/dryad.582sj32
title: Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])

description: Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera:
 Tephritidae) are important pests of many fruits. These flies have been
 spread across the world through global travel and trade, and new areas are
 are at risk of invasion. Whenever new invasive populations are discovered,
 quick and accurate identification is needed to mitigate the damage they
 can cause. Determining invasive pathways can prevent further spread of
 pests as well as subsequent reinvasions through the same pathway.
 Molecular markers can be used for both species identification and pathway
 analysis. We analyzed 1601 individuals from 18 populations using 765 base
 pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the
 haplotype diversity and population structure within these flies from
 across their native and invasive ranges. We analyzed these samples by
 either grouping by species or geographic populations due to the genetic
 similarity in the mitochondrial genome. We found no genetic structure
 between B. dorsalis and B. carambolae and our findings suggest recent and
 most likely ongoing, genetic exchange between these two species in the
 wild. Hyper-diverse mitochondrial genetic diversity in the native range
 suggests large population sizes and relatively high mutation rates. Only
 52% of the haplotypes found in the trap captures from California are
 shared with haplotypes from flies found in our global survey, indicating
 significant genetic diversity in the native range that is missing from our
 samples. However, these results provide a foundation for the accurate
 determination of the provenance of invasive populations around the world.
description: Haplotypes_by_localityVector file of Figure 2Haplotypes_by_localit_new.svgHaplotypes_by_speciesVector file of figure 3Dorsalis_popgen_mtdna_Locality_2018Arlequin file mtDNA grouped by LocalityDorsali_popgen_mtdna_Locality_2018.arpDorsalis_popgen_mtdna_speciesArlequin file mtDNA data grouped by speciesDorsali_popgen_mtdna_species_2018.arp
DOI: 10.5281/zenodo.18389210
title: REVISE-reconstructed sc-SVC
DOI: 10.5281/zenodo.18389211
title: REVISE-reconstructed sc-SVC
DOI: 10.5061/dryad.n2tb31q
title: Data from: Cenozoic evolution of beta diversity and a Pleistocene emergence for modern mammal faunas in China

description: Aim Historical changes in community structure underlie modern spatial
 diversity patterns, but few empirical studies have focused on the
 variation in the community composition of fossil assemblages at large
 spatiotemporal scales. We wanted to investigat how the spatial
 differentiation of mammal communities changed in China throughout the
 Cenozoic in response to tectonic uplift and paleoclimatic changes and
 explore the timing of the emergence of the modern spatially structured
 faunas. Location China Time period Cenozoic (from 65 Ma to the present)
 Major taxa studied Terrestrial mammals Methods We used a compiled database
 of the distributions of fossil and extant mammals to compare the
 multiple-site beta diversity among families and genera within six time
 intervals of the Cenozoic using Sørensen dissimilarity (βsor) and Simpson
 dissimilarity (βsim). To investigate the timing of the emergence of the
 modern spatially structured faunas, we applied hierarchical clustering and
 non-metric multidimensional scaling ordination based on pairwise βsim
 among seven zoogeographical regions within each time slice. Results The
 multiple-site beta diversity at the family level displayed hump-shaped
 changes during the Cenozoic, and it peaked in the Eocene and gradually
 decreased towards the present. However, the genus-level multiple-site beta
 diversity remained rather constant throughout the Cenozoic. Pronounced
 variations in the relationships among the zoogeographical regions were
 revealed in both the cluster analyses and ordinations. The modern spatial
 structure of mammal faunas at the family level was broadly similar to
 those observed in the Pliocene and Pleistocene. Main conclusions The
 spatial differentiation of mammal faunas in China dates back to the Eocene
 and pre-dates the formation of modern topography and climate. Throughout
 the Cenozoic, the spatial structure of mammal faunas was reorganized by an
 interplay of the uplift of the Tibetan Plateau, the emergence of the
 monsoon system and global macroevolutionary processes. The modern
 relationships among zoogeographical regions at the family level were
 established in the Pleistocene.
description: Distributions of fossil
 and extant mammals in China01
 Appendix_occurrence_data; 02 Appendix_community_data_Family; 03
 Appendix_community_data_GenusHe_et_al_2018_Global_Ecology_and_Biogeography.zip
DOI: 10.5061/dryad.n7rm21c
title: Data from: Robust design for coalescent model inference

description: The coalescent process describes how changes in the size or structure of a
 population influence the genealogical patterns of sequences sampled from
 that population. The estimation of (effective) population size changes
 from genealogies that are reconstructed from these sampled sequences is an
 important problem in many biological fields. Often, population size is
 characterized by a piecewise-constant function, with each piece serving as
 a population size parameter to be estimated. Estimation quality depends on
 both the statistical coalescent inference method employed, and on the
 experimental protocol, which controls variables such as the sampling of
 sequences through time and space, or the transformation of model
 parameters. While there is an extensive literature on coalescent inference
 methodology, there is comparatively little work on experimental design.
 The research that does exist is largely simulation-based, precluding the
 development of provable or general design theorems. We examine three key
 design problems: temporal sampling of sequences under the skyline
 demographic coalescent model, spatio-temporal sampling under the
 structured coalescent model, and time discretization for sequentially
 Markovian coalescent models. In all cases, we prove that 1) working in the
 logarithm of the parameters to be inferred (e.g., population size) and 2)
 distributing informative coalescent events uniformly among these
 log-parameters, is uniquely robust. “Robust” means that the total and
 maximum uncertainty of our parameter estimates are minimized, and made
 insensitive to their unknown (true) values. This robust design theorem
 provides rigorous justification for several existing coalescent
 experimental design decisions and leads to usable guidelines for future
 empirical or simulation-based investigations. Given its persistence among
 models, this theorem may form the basis of an experimental design paradigm
 for coalescent inference.
description: Robust coalescent
 designCode for examining
 Fisher experimental design for coalescent processes.robust coalescent design
 examples.zip
DOI: 10.15468/dl.tvvtwd
title: Occurrence Download

description: A dataset containing 97537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "CoordinateUncertaintyInMeters 0.0-350.0",
 "Geometry POLYGON((-0.14651 42.02361,5.13442 42.02361,5.13442 45.25074,-0.14651 45.25074,-0.14651 42.02361))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Amphibia, Squamata)"
 ]
}

 The dataset includes 97537 records from 325 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001530-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m7r60n0
title: Data from: Strong responses from weakly interacting species

description: The impact of species loss from competitive communities partly depends on
 how populations of the surviving species respond. Predicting the response
 should be straightforward using models that describe population growth as
 a function of competitor densities; but these models require accurate
 estimates of interaction strengths. Here, we quantified how well we could
 predict responses to competitor removal in a community of annual plants,
 using a combination of observation and experiment. It was straightforward
 to fit models to multi-species communities, which passed standard
 diagnostic tests and provided apparently sensible estimates of interaction
 strengths. However, the models consistently underpredicted the response to
 competitor removal, by a factor of at least 50%. We argue that this poor
 predictive ability is likely to be general in plant communities due to
 ‘the ghost of competition present’ that confines species to parts of the
 environment in which they compete best.
description: Tuck et al. 2018 Ecology
 Letters dataDataset from Tuck et al.
 2018. Strong Responses From Weakly Interacting Species. Ecology Letters.
 Annual plant population sizes in experimental plots from 2011 to
 2013.Tucketal_StrongResponsesFromWeaklyInteractingSpecies_PlantPopulationSizeData.csv
DOI: 10.5281/zenodo.17763259
title: INRIM_Brand1_10F_2_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 10F SC sample 2 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.17763258
title: INRIM_Brand1_10F_2_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 10F SC sample 2 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.rs39j28
title: Data from: Doping induced dielectric anomaly below the Curie temperature in molecular ferroelectric diisopropylammonium bromide

description: A dielectric anomaly induced by doping has been observed at about 340 K in
 chlorine doped diisopropylammonium bromide (DIPAB-C). The dielectric
 anomaly has a switchable behavior, which indicates potential applications
 on switches and sensors. Temperature dependent Raman spectrum, X-ray
 diffraction and DSC do not show any anomaly around the dielectric anomaly
 temperature, which prove that the dielectric anomaly does not come from
 structure phase transition and has no specific heat variety. It is assumed
 that this relaxation process can be attributed to the freezing of
 ferroelectric domain walls induced by the pinning of point defects.
description: dielectric dsc raman
 xrdArchive.zip
DOI: 10.5061/dryad.22b3c31
title: Data from: A new craniid brachiopod genus from the terminal Ordovician Hirnantia fauna of Myanmar and South China

description: Hirnantian costate craniides are rare in the world and many have only been
 defined using open taxonomic nomenclature. Most of these craniides were
 assigned to the genera Acanthocrania and Philhedra. New material from
 South China and Myanmar forms the basis of a new genus Xenocrania,
 including its type species Palaeocyclus? haimei Reed from the Hirnantia
 fauna in northern Shan State, Myanmar. This genus is characterized by
 unique ornamentation with a large degree of intraspecific variation in
 sympatric and allopatric populations. Three types of ornamentation (A, B
 and C) are recognized within the same population of the same species, and
 even on the same individual. Based on this high degree of variation within
 a single species, we consider Xenocrania haimei and Acanthocrania
 yichangensis Zeng from the Hirnantia fauna of Yichang, western Hubei,
 South China conspecific. X. haimei was probably an opportunistic species,
 exhibiting considerable significant phenotypic pleiotropy (exemplified by
 a highly variable ornament) in response to severe ecological stress,
 particularly during the end Ordovician crisis enabling the species to
 survive the extinction event. Geographically, Xenocrania gen. nov. occurs
 in the Hirnantia fauna not only of Myanmar (Sibumasu) and South China, but
 also of England (Avalonia), Poland (Baltica) and likely Bohemia
 (Perunica). A further reassessment of many nominal or indeterminate taxa
 of Ordovician and Silurian craniides tentatively attributed to Philhedra,
 Acanthocrania and other related genera is needed.
description: Shell measurements of
 Xenocrania haimei (Reed, 1915)This figure Based on
 data from 1) Shuanghe of Changning and 2) Tianbatou and 3) Huangtian of
 Gongxian, southern Sichuan; 4) Miaoquan of Xiushan, southern Chongqing; 5)
 Chaqi of Yichang, western Hubei; and 6) Mandalay Division,
 Myanmar.online figure
 1.tifTotal numbers of ribs or
 spine rays in relation to shell width of Xenocrania haimei (Reed,
 1915)This figure Based on
 data from 1) Shuanghe of Changning and 2) Tianbatou and 3) Huangtian of
 Gongxian, southern Sichuan; 4) Miaoquan of Xiushan, southern Chongqing; 5)
 Chaqi of Yichang, western Hubei; and 6) Mandalay Division,
 Myanmar.online figure
 2.tif
DOI: 10.5281/zenodo.18378848
title: Carola Bridge Collapse Analysis Data
DOI: 10.5281/zenodo.18378847
title: Carola Bridge Collapse Analysis Data
DOI: 10.15468/dl.p245yy
title: Occurrence Download

description: A dataset containing 405 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Living Specimen, Specimen)",
 "TaxonKey is Mellivora capensis"
 ]
}

 The dataset includes 405 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001547-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.