cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hs518
title: Data from: Topological, chemical, and electro-optical characteristics of riboflavin-doped artificial and natural DNA thin films

description: DNA is considered as a useful building bio-material, and it serves as an
 efficient template to align functionalized nanomaterials. Riboflavin
 (RF)-doped synthetic double-crossover DNA (DX-DNA) lattices and natural
 salmon DNA (SDNA) thin films are constructed using substrate assisted
 growth and drop-casting methods, respectively, and their topological,
 chemical, and electro-optical characteristics were evaluated. The critical
 doping concentration of RF ([RF]C, ~5 mM) at given concentrations of
 DX-DNA and SDNA were obtained by observing the phase transition (from
 crystalline to amorphous structures) of DX-DNA and precipitation of SDNA
 in solution above [RF]C. [RF]C are verified by analyzing the atomic force
 microscopy images for DX-DNA and current, absorbance, and
 photoluminescence for SDNA. We study the physical characteristics of
 RF-embedded SDNA thin films, which are the Fourier transform infrared
 (FTIR) spectrum to understand the interaction between the RF and DNA
 molecules, current to evaluate the conductance, absorption to understand
 the RF binding to the DNA, and photoluminescence (PL) to analyze the
 energy transfer between the RF and DNA. The current and UV absorbance band
 of SDNA thin films decrease up to [RF]C followed by an increase above
 [RF]C. In contrast, the PL intensity illustrates the reverse trend, as
 compared to the current and UV absorbance behavior as a function of the
 varying [RF]. Due to the intense PL characteristic of RF, the DNA lattices
 and thin films with RF might offer immense potential to develop efficient
 bio-sensors and useful bio-photonic devices.
description: RF-DNA Raw
 DataFigure
 2(b)_Absorbance-Wavenumber Figure 3_Current-Voltage Figure
 4_Absorbance-Wavelength Figure 5_PL data
DOI: 10.5061/dryad.4411b
title: Data from: Species-driven phases and increasing structure in early-successional plant communities

description: Successional phases describe changes in ecological communities that
 proceed in steps rather than continuously. Despite their importance for
 the understanding of ecosystem development, there still exists no reliable
 definition of phases and no quantitative measure of phase transitions. In
 order to obtain these data, we investigated primary succession in an
 artificial catchment (6 ha) in eastern Germany over a period of 6 years.
 The data set consists of records of plant species and their cover values,
 and initial substrate properties, both from plots in a regular grid (20 m
 × 20 m) suitable for spatial data analysis. Community assembly was studied
 by analyses of species co-occurrence and nestedness. Additionally, we
 correlated lognormal and log series distributions of species abundance to
 each community. We here introduce a new general method for detection of
 successional phases based on the degree of transient spatial homogeneity
 in the study system. Spatially coherent vegetation patterns revealed
 nonoverlapping partitions within this sequence of primary succession and
 were characterized as two distinct ecological phases. Patterns of species
 co-occurrence were increasingly less random, and hence the importance of
 demographic stochasticity and neutral community assembly decreased during
 the study period. Our findings highlight the spatial dimension of
 successional phases and quantify the degree of change between these steps.
 They are an element for advancing a more reliable terminology of
 ecological successions.
description: species_matrices_SCT-1_1m²_&_25m²_plotsGiven are the cover values [in %] of the vascular species and bryophytes recorded on the permanent plots at the SCT-1 part of the Chicken Creek catchment (see fig. 1) in the study period.species_matrices_SCT-2_1m²_&_25m²_plotsGiven are the cover values [in %] of the vascular species and bryophytes recorded on the permanent plots at the SCT-2 part of the Chicken Creek catchment (see fig. 1) in the study period.environment_matrices_SCT-1_1m²+25m²Given are the environmental parameters measured on the permanent plots at the SCT-1 part of the Chicken Creek catchment after its construction in 2005 (see methods).environment_matrices_SCT-2_1m²+25m²Given are the environmental parameters measured on the permanent plots at the SCT-2 part of the Chicken Creek catchment after its construction in 2005 (see methods).
DOI: 10.5061/dryad.qh7k8
title: Data from: First- and second-order sociality determine survival and reproduction in cooperative cichlids

description: Cooperative breeders are model organisms for the study of cooperation. The
 costs and benefits involved in cooperation are typically scrutinised only
 at the group level. However, multi-level social organisations, involving
 interactions among individuals at various levels, are often observed. To
 understand the adaptive value of cooperation and the evolution of complex
 social organisation, the importance of different levels of social
 organisation for direct and indirect fitness components should be
 identified. Here we show that in the cooperatively breeding, colonial
 cichlid fish Neolamprologus pulcher, both large group size and high colony
 density significantly raise group persistence and productivity. On the
 individual level, however, survival is not significantly affected by group
 size or local density. Yet, breeders in large groups benefit from lower
 population density by an increased reproductive rate, while breeders in
 smaller groups have greater reproduction in denser areas. Indirect fitness
 gains from cooperation are apparently small for subordinate helpers,
 whereas they gain direct fitness by improved chances to survive and breed
 independently in the future. This highlights that complex forms of
 sociality and costly cooperation may evolve in the absence of large
 indirect benefits and the influence of kin selection.
description: MsJungwirth5ProcBDataAn excel file containing all long-term data of groups and individuals and the respective fitness estimates which are described in the manuscript
DOI: 10.5061/dryad.44m2h
title: Data from: Does habitat specialization shape the evolutionary potential of wild bird populations?

description: Because specialist species evolved in more temporally and spatially
 homogeneous environments than generalist species, they are supposed to
 experience less fluctuating selection. For this reason, we expect
 specialists to show lower overall genetic variation as compared to
 generalists. We also expect populations from specialist species to be
 smaller and more fragmented, with lower neutral genetic diversity. We
 tested these hypotheses by investigating patterns of genetic diversity
 along a habitat specialization gradient in wild birds, based on estimates
 of heritability, coefficients of variation of additive genetic variance,
 and heterozygosity available in the literature. We found no significant
 effect of habitat specialization on any of the quantitative genetic
 estimators but generalists had higher heterozygosity. This effect was
 mainly a consequence of the larger population size of generalists. Our
 results suggest that evolutionary potential does not differ at the
 population level between generalist and specialist species, but the trend
 observed in heterozygosity levels and population sizes may explain their
 difference in susceptibility to extinction.
description: data for SSI
 specialization indexHeritability, CVa and
 Heterozygosity of wild bird populations associated with SSI specialization
 index.dataSSI.xlsdata for niche widthHeritability, CVa and Heterozygosity for wild bird populations assiciated with niche width.data theta.xls
DOI: 10.5061/dryad.983b0
title: Data from: Strong natural selection on juveniles maintains a narrow adult hybrid zone in a broadcast spawner

description: Natural selection can maintain and help form species across different
 habitats, even when dispersal is high. Selection against inferior migrants
 (immigrant inviability) acts when locally adapted populations suffer high
 mortality on dispersal to unsuitable habitats. Habitat-specific
 populations undergoing divergent selection via immigrant inviability
 should thus show (1) a change in the ratio of adapted to nonadapted
 individuals among age/size classes and (2) a cline (defined by the
 environmental gradient) as selection counterbalances migration. Here we
 examine the frequencies of two depth-segregated lineages in juveniles and
 adults of a Caribbean octocoral, Eunicea flexuosa. Distributions of the
 two lineages in both shallow and deep environments were more distinct when
 inferred from adults than juveniles. Despite broad larval dispersal, we
 also found an extremely narrow hybrid zone (&lt;100 m), with
 coincident clines for molecular and morphological characters of the host
 coral and its algal symbiont. Effective dispersal estimates derived from
 the hybrid zone are remarkably small (&lt;20 m) for a broadcast
 spawner. The large selection coefficient against mismatched genotypes
 derived from cohort data is consistent with that from field transplant
 experiments. Narrow hybrid zones and limited effective dispersal may be a
 common outcome of long periods of postsettlement, prereproductive
 selection across steep ecological gradients. Strong diversifying selection
 provides a mechanism to explain the prevalence of depth-segregated sibling
 species in the sea.
description: Juvenile_adult_genotypesContains genotypic data for juveniles and adults, including DNA sequence for both msh and i3p.564Alignment for gene 564.gly3pAlignment for Glyceraldehyde-3-phosphate dehydrogenase (g3p)I3PAlignment for Inositol 3- phosphatase (i3p)EF1AAlignment for Elongation Factor 1 alpha (ef1)ct2Alignment for Calcium transporter 2 (ct2)1633.phymshAlignment for the mitochondrial mismatch repair gene (msh)HZAR_cline_character_frequenciesInput file used for HZAR. Contains frequency data for all characters, including host and symbiont genotypes and host morphologyHZAR locationsContains the information about the distance in the transect for each populationeflexuosaLocationspsbAAlignment for psbA of Symbiodinium B1
DOI: 10.5061/dryad.8t70r
title: Data from: First-principles calculations of structural, electronic, magnetic and elastic properties of Mo2FeB2 under high pressure

description: The structural and electronic density of states, magnetic, and elastic
 properties of Mo2FeB2 under high pressure have been investigated with
 first principles calculations. Furthermore, the thermal dynamic properties
 of Mo2FeB2 were also studied with the quasiharmonic Debye model. The
 volume of Mo2FeB2 decreases with the increasing pressure. Using the
 analysis of the density of the states, atom population and Mulliken
 overlap population, it is observed that as the pressure increases, the B-B
 bonds are strengthened, and the B-Mo covalency decreases. Moreover, for
 all pressures, Mo2FeB2 is detected in the antiferromagnetic phase and the
 magnetic moments decrease with the increasing pressure. The calculated
 bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio and
 universal anisotropy index all increase with the increasing pressure. From
 thermal expansion coefficient analysis, it is found that Mo2FeB2 shows
 good volume invariance under high pressure and temperature. The
 examination of the dependence of heat capacity on the temperature and
 pressure shows that heat capacity is more sensitive to temperature than to
 pressure
description: Figures
 dataFigures.rarfractional coordinatesThis the table for fractional coordinates of atoms under different pressures.
DOI: 10.5061/dryad.4b0sr
title: Data from: Nuclear magnetic resonance measurements of velocity distributions in an ultrasonically vibrated granular bed

description: We report the results of nuclear magnetic resonance imaging experiments on
 granular beds of mustard grains fluidized by vertical vibration at
 ultrasonic frequencies. The variation of both granular temperature and
 packing fraction with height was measured within the three-dimensional
 cell for a range of vibration frequencies, amplitudes and numbers of
 grains. Small increases in vibration frequency were found—contrary to the
 predictions of classical ‘hard-sphere’ expressions for the energy flux
 through a vibrating boundary—to result in dramatic reductions in granular
 temperature. Numerical simulations of the grain–wall interactions, using
 experimentally determined Hertzian contact stiffness coefficients, showed
 that energy flux drops significantly as the vibration period approaches
 the grain–wall contact time. The experiments thus demonstrate the need for
 new models for ‘soft-sphere’ boundary conditions at ultrasonic
 frequencies.
description: Data for Figures 5, 9
 and 10Please see the ReadMe
 file for a full description.data.zip
DOI: 10.5061/dryad.2j1f3
title: Data from: Predicting forest insect flight activity: a Bayesian network approach

description: Daily flight activity patterns of forest insects are influenced by
 temporal and meteorological conditions. Temperature and time of day are
 frequently cited as key drivers of activity; however, complex interactions
 between multiple contributing factors have also been proposed. Here, we
 report individual Bayesian network models to assess the probability of
 flight activity of three exotic insects, Hylurgus ligniperda, Hylastes
 ater, and Arhopalus ferus in a managed plantation forest context. Models
 were built from 7,144 individual hours of insect sampling, temperature,
 wind speed, relative humidity, photon flux density, and temporal data.
 Discretized meteorological and temporal variables were used to build naïve
 Bayes tree augmented networks. Calibration results suggested that the H.
 ater and A. ferus Bayesian network models had the best fit for low Type I
 and overall errors, and H. ligniperda had the best fit for low Type II
 errors. Maximum hourly temperature and time since sunrise had the largest
 influence on H. ligniperda flight activity predictions, whereas time of
 day and year had the greatest influence on H. ater and A. ferus activity.
 Type II model errors for the prediction of no flight activity is improved
 by increasing the model’s predictive threshold. Improvements in model
 performance can be made by further sampling, increasing the sensitivity of
 the flight intercept traps, and replicating sampling in other regions.
 Predicting insect flight informs an assessment of the potential
 phytosanitary risks of wood exports. Quantifying this risk allows
 mitigation treatments to be targeted to prevent the spread of invasive
 species via international trade pathways.
description: Flight activity case
 fileThis .csv file is the
 full case file that was used to create Bayesian network models of flight
 activity. The file includes both the mean catch per hour of the three
 target species and the meteorological and site
 information.mean_hourly_flight_activity_FINAL_26-5-17.csv
DOI: 10.5061/dryad.nh30v
title: Data from: New approaches to the biogeography and areas of endemism of red oaks (Quercus L., section Lobatae)

description: An area of endemism is defined by the spatial congruence among two or more
 species with distributions that are limited by barriers. In this study, we
 explored and discussed the use of the network analysis method (NAM) and
 neighbor-joining (NJ) to analyze the areas of endemism of Quercus sect.
 Lobatae (red oak species) in Mexico and Central America. We compared the
 NAM and NJ with other methods commonly used in biogeographic studies to
 show the advantages of these new approaches and to identify the
 shortcomings of other approaches. The NAM used in this study is based on
 notions of centrality measures, such as betweenness. We incorporated the
 strength of the ties within the internal networks through p-cores and
 aggregate constraints in iterative analyses. The NAM based on betweenness
 is ideal for recognizing completely allopatric areas of endemism. The
 iterative NAMs increase the number of possible areas of endemism because
 they minimize the effect of minimal overlap, and the p-core is efficient
 at identifying the closest relationships among species in the cases in
 which betweenness is not informative. The number of areas of endemism
 increases when the sympatry matrix minimizes the dispersal effect and the
 sample effort is maximized, allowing the identification of the greatest
 number of these areas. The NJ method supports the idea that areas diverge
 among themselves in a differential way; the long branches correspond to
 zones with high speciation rates and complex histories (biotic and
 tectonic), and the short branches correspond to zones with low speciation
 rates and simple histories. In a classification scheme, NJ was capable of
 identifying the areas that are considered biotically complex because of
 their high speciation rates. The results obtained with the NAM and NJ
 showed that the physiographic regions of Mexico are not natural units and
 that many of them are composed of at least two different biotic
 components.
description: Appendix
 1Three sympatry matrices
 used in the network analysis of 72 species of red oaks.Appendix
 2Two
 matrices: (1) presence/absence using NJ, PAE, and clusters (UPGMA)
 analyses, and (b) with the inverse of the distribution for NJ analysis for
 72 red oaks.Appendix
 3
DOI: 10.5061/dryad.74gd7
title: Data from: Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

description: Disruption of naturally evolved spatial patterns of genetic variation and
 local adaptations is a growing concern in wildlife management and
 conservation. During the last decade, releases of native taxa with
 potentially non-native genotypes have received increased attention. This
 has mostly concerned conservation programs, but releases are also widely
 carried out to boost harvest opportunities. The mallard, Anas
 platyrhynchos, is one of few terrestrial migratory vertebrates subjected
 to large-scale releases for hunting purposes. It is the most numerous and
 widespread duck in the world, yet each year more than three million farmed
 mallard ducklings are released into the wild in the European Union alone
 to increase the harvestable population. This study aimed to determine the
 genetic effects of such large-scale releases of a native species,
 specifically if wild and released farmed mallards differ genetically among
 subpopulations in Europe, if there are signs of admixture between the two
 groups, if the genetic structure of the wild mallard population has
 changed since large-scale releases began in the 1970s, and if the current
 data matches global patterns across the Northern hemisphere. We used
 Bayesian clustering (Structure software) and Discriminant Analysis of
 Principal Components (DAPC) to analyze the genetic structure of historical
 and present-day wild (n = 171 and n = 209, respectively) as well as farmed
 (n = 211) mallards from six European countries as inferred by 360
 single-nucleotide polymorphisms (SNPs). Both methods showed a clear
 genetic differentiation between wild and farmed mallards. Admixed
 individuals were found in the present-day wild population, implicating
 introgression of farmed genotypes into wild mallards despite low survival
 among released farmed mallards. Such cryptic introgression would alter the
 genetic composition of wild populations and may have unknown long-term
 consequences for conservation.
description: Supplementary Structure
 input fileGenotype calls for all
 sampled individuals. SNP numpers in columns and individuals in rows.
 Genotype calls (1-4) corresponds to bases A, T, C, and G respectively. The
 file works as an input file in Structure
DOI: 10.5061/dryad.43g64
title: Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales

description: The research field of comparative genomics is moving from a focus on genes
 to a more holistic view including the repetitive complement. This study
 aimed to characterize relative proportions of the repetitive fraction of
 large, complex genomes in a non-model system. The monocotyledonous plant
 order Asparagales (onion, asparagus, agave) comprises some of the largest
 angiosperm genomes and represents variation in both genome size and
 structure (karyotype). Anonymous, low coverage, single-end Illumina data
 from eleven exemplar Asparagales taxa were assembled using a de novo
 method. Resulting contigs were annotated using a reference library of
 available monocot repetitive sequences. Mapping reads to contigs provided
 rough estimates of relative proportions of each type of transposon in the
 nuclear genome. The results were parsed into general repeat types and
 synthesized with genome size estimates and a phylogenetic context to
 describe the pattern of transposable element evolution among these
 lineages. The major finding is that while some lineages in Asparagales
 exhibit conservation in repeat proportions, there is generally wide
 variation in types and frequency of repeats. This approach is an
 appropriate first step in characterizing repeats in evolutionary lineages
 with a paucity of genomic resources.
description: Asparagales
DOI: 10.5061/dryad.bq70c
title: Data from: Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers

description: Poeciliids are a diverse group of small Neotropical fishes, and despite
 considerable research attention as models in ecology and evolutionary
 biology, our understanding of their biogeographic and phylogenetic
 relationships is still limited. We investigated the phylogenetic
 relationships of South and Central American Poecilia, by examining 2395
 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for
 18 species across six subgenera. Fifty-eight novel sequences were acquired
 from newly collected specimens and 20 sequences were obtained from
 previously published material. Analyses of concatenated and partitioned
 mitochondrial DNA and nuclear DNA sets resulted in a well-supported
 phylogeny that resolved several monophyletic groups corresponding to
 previously hypothesized subgenera and species complexes.
description: Dataset 1: Main
 PhylogenyData used to generate
 Figure 1.1a]_Dataset_1_Figure_1.nexFigure 1, BINewick Tree File for Fig. 1, BI with FigTree Annotations1b]_NewickTree1_Fig1_BI.treFigure 1, MLNewick Tree File for Fig. 1, ML with FigTree Annotations1b]_NewickTree2_Fig1_ML.treDataset 2, Divergence Time EstimateData used to generate Figure 2.2a]_Dataset_2_Figure_2.nexFigure 2Newick Tree File for Fig. 2 with FigTree Annotations2b]_NewickTree3_Fig2.treDataset S1, mtDNA PhylogenyData used to generate Figure S13a]_Dataset_S1_Figure_S1_mtDNA.nexFigure S1, BINewick Tree File for Fig. S1, BI with FigTree Annotations3b]_NewickTree4_FigS1_BI.treFigure S1, MLNewick Tree File for Fig. S1, ML with FigTree Annotations3c]_NewickTree5_FigS1_ML.treDataset S2, nDNA PhylogenyData used to generate Figure S24a]_Dataset_S2_Figure_S2__nDNA.nexFigure S2, BINewick Tree File for Fig. S2, BI with FigTree Annotations4b]_NewickTree6_FigS2_BI.treFigure S2, MLNewick Tree File for Fig. S2, ML with FigTree Annotations4c]_NewickTree6_FigS2_ML.treTable 25]_Table2.csvTable S15]_TableS1.csv