cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c763m
title: Data from: Relationships among taxonomic, functional, and phylogenetic ant diversity across the biogeographic regions of Europe

description: Understanding how different biodiversity components are related across
 different environmental conditions is a major goal in macroecology and
 conservation biogeography. We investigated correlations among alpha and
 beta taxonomic (TD), phylogenetic (PD), and functional diversity (FD) in
 ant communities in the five biogeographic regions most representative of
 western Europe; we also examined the degree of niche conservatism. We
 combined data from 349 ant communities composed of 154 total species,
 which were characterized by 10 functional traits and by phylogenetic
 relatedness. We computed TD, PD, and FD using the Rao quadratic entropy
 index, which allows each biodiversity component to be partitioned into α
 and β diversity within the same mathematical framework. We ran generalized
 least squares and multiple matrix regressions with randomization to
 investigate relationships among the diversity components. We used
 Pagel's λ test to explore niche conservatism in each biogeographic
 region. At the alpha scale, TD was consistently, positively related to PD
 and FD, although the strength and scatter of this relationship changed
 among the biogeographic regions. Meanwhile, PD and FD consistently matched
 up across regions. Accordingly, we found similar degrees of niche
 conservatism across regions. Nonetheless, these alpha-scale relationships
 had low coefficients of determination. At the beta scale, the three
 diversity components were highly correlated across all regions (especially
 TD and FD, as well as PD and FD). Our results imply that the different
 diversity components, and especially PD and FD, are consistently related
 across biogeographic regions and analytical scale. However, the
 alpha-scale relationships were quite weak, suggesting environmental
 factors might influence the degree of association among diversity
 components at the alpha level. In conclusion, conservation programs should
 seek to preserve functional and phylogenetic diversity in addition to
 species richness, and this approach should be applied universally,
 regardless of the biogeographic locations of the sites to be protected.
description: Ant species occurrence
 and site characterizationThis data file include
 details of ant species occurrence for 349 European sites as well as the
 latitude and longitude and the biogeographic region corresponding to these
 sites. Further details are provided in the paper.Data Arnan et
 al.xlsx
DOI: 10.5061/dryad.152
title: Data from: Papers from the Hopkins-Stanford Galapagos Expedition, 1898-99. XVI. Birds.

description: [No abstract entered]
description: Morphological
 Measurements of Galapagos FinchesA large collection of
 morphological measurements for Galapagos finches.morphSnodgrassHeller.TABmorphSnodgrassHeller.xls
DOI: 10.5061/dryad.tq0qc
title: Data from: Tweeting birds: online mentions predict future citations in ornithology

description: The rapid growth of online tools to communicate scientific research raises
 the important question of whether online attention is associated with
 citations in the scholarly literature. The Altmetric Attention Score (AAS)
 quantifies the attention received by a scientific publication on various
 online platforms including news, blogs and social media. It has been
 advanced as a rapid way of gauging the impact of a piece of research, both
 in terms of potential future scholarly citations and wider online
 engagement. Here, we explore variation in the AAS of 2677 research
 articles published in 10 ornithological journals between 2012 and 2016. On
 average, AAS increased sevenfold in just five years, primarily due to
 increased activity on Twitter which contributed 75% of the total score.
 For a subset of 878 articles published in 2014, including an additional
 323 ornithology articles from non-specialist journals, an increase in AAS
 from 1 to 20 resulted in a predicted 112% increase in citation count from
 2.6 to 5.5 citations per article. This effect interacted with journal
 impact factor, with weaker effects of AAS in higher impact factor
 journals. Our results suggest that altmetrics (or the online activity they
 measure), as well as complementing traditional measures of scholarly
 impact in ornithology such as citations, may also anticipate or even drive
 them.
description: data_ornithologyAltmetric and citation data for 2667 articles from 10 ornithology journals (2012-2016). 'jif' is 2015 journal impact factor, 'score' is Altmetric Attention Scoredata_citesAltmetric and citation data for 878 articles from 10 ornithological journals and 15 non-specialist journals (2014). 'jif' is 2015 journal impact factor, 'score' is Altmetric Attention Score.script v2Reproducible R code for manipulating, analysing and plotting the data.script_v2.R
DOI: 10.5061/dryad.v10d218
title: Data from: Gigapixel big data movies provide cost‐effective seascape scale direct measurements of open‐access coastal human use such as recreational fisheries

description: Collecting data on unlicensed open‐access coastal activities, such as some
 types of recreational fishing, has often relied on telephone interviews
 selected from landline directories. However, this approach is becoming
 obsolete due to changes in communication technology such as a switch to
 unlisted mobile phones. Other methods, such as boat ramp interviews, are
 often impractical due to high labor cost. We trialed an autonomous,
 ultra‐high‐resolution photosampling method as a cost effect solution for
 direct measurements of a recreational fishery. Our sequential
 photosampling was batched processed using a novel software application to
 produce “big data” time series movies from a spatial subset of the
 fishery, and we validated this with a regional bus‐route survey and
 interviews with participants at access points. We also compared labor
 costs between these two methods. Most trailer boat users were recreational
 fishers targeting tuna spp. Our camera system closely matched trends in
 temporal variation from the larger scale regional survey, but as the
 camera data were at much higher frequency, we could additionally describe
 strong, daily variability in effort. Peaks were normally associated with
 weekends, but consecutive weekend tuna fishing competitions led to an
 anomaly of high effort across the normal weekday lulls. By reducing field
 time and batch processing imagery, Monthly labor costs for the camera
 sampling were a quarter of the bus‐route survey; and individual camera
 samples cost 2.5% of bus route samples to obtain. Gigapixel panoramic
 camera observations of fishing were representative of the temporal
 variability of regional fishing effort and could be used to develop a
 cost‐efficient index. High‐frequency sampling had the added benefit of
 being more likely to detect abnormal patterns of use. Combinations of
 remote sensing and on‐site interviews may provide a solution to describing
 highly variable effort in recreational fisheries while also validating
 activity and catch.
description: Fortescue
 GigaPan_ver2Excel datasheet,
 includes some analysis
DOI: 10.5061/dryad.9112
title: Data from: The Bantu expansion revisited: a new analysis of Y chromosome variation in Central Western Africa

description: The current distribution of Bantu languages is commonly considered to be a
 consequence of a relatively recent population expansion (3-5 kya) in
 Central Western Africa. While there is a substantial consensus regarding
 the centre of origin of Bantu languages (the Benue River Valley, between
 South East Nigeria and Western Cameroon), the identification of the area
 from where the population expansion actually started, the relation between
 the processes leading to the spread of languages and peoples and the
 relevance of local migratory events remain controversial. In order to shed
 new light on these aspects, we studied Y chromosome variation in a broad
 dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo.
 Our results evidence an evolutionary scenario which is more complex than
 had been previously thought, pointing to a marked differentiation of
 Cameroonian populations from the rest of the dataset. In fact, in contrast
 with the current view of Bantu speakers as a homogeneous group of
 populations, we observed an unexpectedly high level of inter-population
 genetic heterogeneity and highlighted previously undetected diversity for
 lineages associated with the diffusion of Bantu languages (E1b1a (M2)
 sub-branches). We also detected substantial differences in local
 demographic histories, which concord with the hypotheses regarding an
 early diffusion of Bantu languages into the forest area and a subsequent
 demographic expansion and migration towards eastern and western Africa.
description: Y chromosome SNPs and
 STRsThe file contains 17
 SNPs loci and 14 STRs loci
DOI: 10.5061/dryad.6r0p6s2
title: Data from: A conservation hatchery population of Delta Smelt shows evidence of genetic adaptation to captivity after 9 generations

description: Genetic adaptation to captivity is a concern for threatened and endangered
 species held in conservation hatcheries. Here, we present evidence of
 genetic adaptation to captivity in a conservation hatchery for the
 endangered Delta Smelt (Fish Conservation and Culture Laboratory,
 University of California Davis; FCCL). The FCCL population is genetically
 managed with parentage analysis and the addition of wild fish each year.
 Molecular monitoring indicates little loss of genetic variation and low
 differentiation between the wild and conservation populations. Yet, we
 found an increase in offspring survival to reproductive maturity during
 the subsequent spawning season (recovery rate) in crosses that included
 one or both cultured parents. Crosses with higher levels of hatchery
 ancestry tend to produce a greater number of offspring that are recovered
 the following year. The recovery rate of a cross decreases when offspring
 are raised in a tank with fish of high levels of hatchery ancestry. We
 suggest changes in fish rearing practices at the FCCL to reduce genetic
 adaptation to captivity, as Delta Smelt numbers in the wild continue to
 decline and the use of FCCL fish for reintroduction becomes more likely.
description: Primary
 DataPrimary data includes
 pedigree file from F1 to F9 generations, including cross type (wild,
 cultured), domestication index, and recovery data. Contact
 ajfinger@ucdavis.edu for any questions.Data
 availability.xlsx
DOI: 10.5061/dryad.5sb1219
title: Data from: Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan

description: Climatic changes have played major roles in plants’ evolutionary history.
 Glacial oscillations have been particularly important, but some of their
 effects on plants’ populations are poorly understood, including the
 numbers and locations of refugia in Asian warm temperate zones. In the
 present study, we investigated the demographic history of the broadleaved
 evergreen tree species Castanopsis sieboldii (Fagaceae) during the last
 glacial period in Japan. We used approximate Bayesian computation (ABC)
 for model comparison and parameter estimation for the demographic
 modelling using 27 EST associated microsatellites. We also performed the
 species distribution modelling (SDM). The results strongly support a
 demographic scenario that the Ryukyu Islands and the western parts in the
 main islands (Kyushu and western Shikoku) were derived from separate
 refugia and the eastern parts in the main islands and the Japan Sea groups
 were diverged from the western parts prior to the coldest stage of the
 Last Glacial Maximum (LGM). Our data indicate that multiple refugia
 survived at least one in the Ryukyu Islands, and the other three regions
 of the western and eastern parts and around the Japan Sea of the main
 islands of Japan during the LGM. The SDM analysis also suggests the
 potential habitats under LGM climate conditions were mainly located along
 the Pacific Ocean side of coastal region. Our ABC-based study helps
 efforts resolve the demographic history of a dominant species in warm
 temperate broadleaved forests during and after the last glacial period,
 which provides a basic model for future phylogeographical studies using
 this approach.
description: Genotypes of Castanopsis
 sieboldii individuals and population informationGenotype data (27
 EST-SSR markers) for 792 Castanopsis sieboldii individuals from 33
 populations33Cs27loci_repeat2_and_pop.xlsxabc_fsc2_180421R and shell scripts for ABC analyses of four populations of Castanopsis sieboldii (Aoki et al. 2018).
DOI: 10.5061/dryad.gh0q91j
title: Data from: Accounting for differences in species frequency distributions when calculating beta diversity in the fossil record

description: 1. Beta diversity is a measure of the taxonomic differentiation between
 habitats/localities within an assemblage, and is normally calculated as a
 set of pairwise taxonomic “distances” between the localities. 2. Due to
 the incomplete sampling, beta diversity estimates for fossil assemblages
 will always be higher than the true value. However, the difference between
 the observed and true distances will vary greatly depending on differences
 in the shape of the relative abundance distribution. 3. Using simulations,
 it is shown that incomplete sampling of a homogenous fauna with more even
 relative abundances of taxa produces higher beta diversity than one with
 very few extremely common taxa. 4. A new procedure is proposed for
 calculating beta diversity in the fossil record, whereby the observed
 distances are compared to the distance obtained by randomly resampling a
 homogenous fauna with the same abundance distribution. This procedure is
 named Relative Abundance Corrected beta diversity (RAC beta diversity).
 Simulations indicate that this method outperforms raw beta diversity
 estimates, providing beta diversity estimates closer to the true values
 even when the assumptions of the method are violated. 5. This method is
 applied to an empirical dataset: Permian-Triassic tetrapods from the Karoo
 Supergroup of South Africa. Increased provincialism is found across the
 Permian-Triassic boundary in contrast to uncorrected beta diversity
 patterns.
description: Supplementary Data 1 -
 Eodicynodon AZSpecimens from the
 Eodicynodon assemblage zone, their locality of provenance and taxonomic
 assignmentSupplementary Data 2 -
 Tapinocephalus AZSpecimens from the
 Tapinocephalus assemblage zone, their locality of provenance and taxonomic
 assignmentSupplementary Data 3 -
 Pristerognathus AZSpecimens from the
 Pristerognathus assemblage zone, their locality of provenance and
 taxonomic assignmentSupplementary Data 4 -
 Tropidostoma AZSpecimens from the
 Tropidostoma assemblage zone, their locality of provenance and taxonomic
 assignmentSupplementary Data 5 -
 Cistecephalus AZSpecimens from the
 Cistecephalus assemblage zone, their locality of provenance and taxonomic
 assignmentSupplementary Data 6 -
 Daptocephalus AZSpecimens from the
 Daptocephalus assemblage zone, their locality of provenance and taxonomic
 assignmentSupplementary Data 7 -
 Lysterosaurus AZSpecimens from the
 Lystrosaurus assemblage zone, their locality of provenance and taxonomic
 assignmentSupplementary Data 8 -
 Cynognathus AZSpecimens from the
 Cynognathus assemblage zone, their locality of provenance and taxonomic
 assignmentSupplementary Data
 9_revisedR functions for
 calculating the modified Forbes distance metric and calculating the
 Relative-abundance-corrected beta diversityInstructions for RAC
 FunctionInstructions for
 calculating the RAC Beta Diversity estimate using the R function
 (supplementary data 9)Example
 datasetThe example dataset for
 use in the example analyses
DOI: 10.5061/dryad.qm96r
title: Data from: Spectroscopic analysis of myoglobin and cytochrome c dynamics in isolated cardiomyocytes during hypoxia and reoxygenation

description: Raman microspectroscopy was applied to monitor the intracellular redox
 state of myoglobin and cytochrome c from isolated adult rat cardiomyocytes
 during hypoxia and reoxygenation. The nitrite reductase activity of
 myoglobin leads to the production of nitric oxide in cells under hypoxic
 conditions, which is linked to the inhibition of mitochondrial
 respiration. In this work, the subsequent reoxygenation of cells after
 hypoxia is shown to lead to increased levels of oxygen-bound myoglobin
 relative to the initial levels observed under normoxic conditions.
 Increased levels of reduced cytochrome c in ex vivo cells are also
 observed during hypoxia and reoxygenation by Raman microspectroscopy. The
 cellular response to reoxygenation differed dramatically depending on the
 method used in the preceding step to create hypoxic conditions in the cell
 suspension, where a chemical agent, sodium dithionite, leads to reduction
 of cytochromes in addition to removal of dissolved oxygen, and bubbling-N2
 gas leads to displacement of dissolved oxygen only. These results have an
 impact on the assessment of experimental simulations of hypoxia in cells.
 The spectroscopic technique employed in this work will be used in the
 future as an analytical method to monitor the effects of varying levels of
 oxygen and nutrients supplied to cardiomyocytes during either the
 preconditioning of cells or the reperfusion of ischaemic tissue.
description: DatasetsFull contents of data presented in figures 1-5
DOI: 10.5061/dryad.3428j
title: Data from: Further development of the Assessment of Military Multitasking Performance: iterative reliability testing

description: The Assessment of Military Multitasking Performance (AMMP) is a battery of
 functional dual-tasks and multitasks based on military activities that
 target known sensorimotor, cognitive, and exertional vulnerabilities after
 concussion/mild traumatic brain injury (mTBI). The AMMP was developed to
 help address known limitations in post concussive return to duty
 assessment and decision making. Once validated, the AMMP is intended for
 use in combination with other metrics to inform duty-readiness decisions
 in Active Duty Service Members following concussion. This study used an
 iterative process of repeated interrater reliability testing and
 feasibility feedback to drive modifications to the 9 tasks of the original
 AMMP which resulted in a final version of 6 tasks with metrics that
 demonstrated clinically acceptable ICCs of &gt; 0.92 (range of
 0.92–1.0) for the 3 dual tasks and &gt; 0.87 (range 0.87–1.0) for the
 metrics of the 3 multitasks. Three metrics involved in recording subject
 errors across 2 tasks did not achieve ICCs above 0.85 set apriori for
 multitasks (0.64) and above 0.90 set for dual-tasks (0.77 and 0.86) and
 were not used for further analysis. This iterative process involved 3
 phases of testing with between 13 and 26 subjects, ages 18–42 years,
 tested in each phase from a combined cohort of healthy controls and
 Service Members with mTBI. Study findings support continued validation of
 this assessment tool to provide rehabilitation clinicians further return
 to duty assessment methods robust to ceiling effects with strong face
 validity to injured Warriors and their leaders.
description: Phase III_FortBragg_IRR
 Database_Dec2014This is an Excel
 spreadsheet of IRR reliability data Phase III. It is one of 4 Excel files
 and a data dictionary file.Phase Ia_AMMP IRR
 USARIEM V1 6DEC_2012This is an Excel data
 file for the interrater reliability testing in Phase Ia of this study.
 There are 4 data files for different phases of this study and a data
 dictionary.Phase Ib AMMP IRR
 USARIEM SALUT_CQ_May 2013This is an Excel data
 file for the interrater reliability testing in Phase Ib of this study.
 There are 4 data files for different phases of this study and a data
 dictionary.Phase II_AMMP Bragg IRR
 November2013This is an Excel file
 for Phase II interrater reliability testing, there are 4 data files and
 one data dictionary file.AMMP REDCap data
 dictionary_DRYAD_16Dec2016Data dictionary for IRR
 study.
DOI: 10.5061/dryad.b003f
title: Data from: Low plant density enhances gene dispersal in the Amazonian understory herb Heliconia acuminata

description: In theory, conservation genetics predicts that forest fragmentation will
 reduce gene dispersal, but in practice, genetic and ecological processes
 are also dependent on other population characteristics. We used Bayesian
 genetic analyses to characterize parentage and propagule dispersal in
 Heliconia acuminata L. C. Richard (Heliconiaceae), a common Amazonian
 understory plant that is pollinated and dispersed by birds. We studied
 these processes in two continuous forest sites and three 1-ha fragments in
 Brazil's Biological Dynamics of Forest Fragments Project. These sites
 showed variation in the density of H. acuminata. Ten microsatellite
 markers were used to genotype flowering adults and seedling recruits and
 to quantify realized pollen and seed dispersal distances, immigration of
 propagules from outside populations, and reproductive dominance among
 parents. We tested whether gene dispersal is more dependent on
 fragmentation or density of reproductive plants. Low plant densities were
 associated with elevated immigration rates and greater propagule dispersal
 distances. Reproductive dominance among inside-plot parents was higher for
 low density than for high density populations. Elevated local flower and
 fruit availability is probably leading to spatially more proximal bird
 foraging and propagule dispersal in areas with high density of
 reproductive plants. Nevertheless, genetic diversity, inbreeding
 coefficients and fine-scale spatial genetic structure were similar across
 populations, despite differences in gene dispersal. This result may
 indicate that the opposing processes of longer dispersal events in
 low-density populations versus higher diversity of contributing parents in
 high-density populations balance the resulting genetic outcomes and
 prevent genetic erosion in small populations and fragments.
description: microsat_location_HacuminataThis is an excel file that contains 3 spreadsheets with data on location, microsatellite genotypes and ecological information (number of flowers, seeds, year of flowering and recruitment) of the understory plant Heliconia acuminata. Data were collected in the Biological Dynamics of Forest Fragments Project, Manaus, Brazil. For more information see the readme file.genedispersalmodel_code_CortesCode with R script to estimate pollen and seed dispersal parameters and pedigree of Heliconia acuminata