cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n8pk0p2rb
title: Legacy forest structure increases bird diversity and abundance in aging young forests

description: Many studies have demonstrated the importance of early successional forest
 habitat for breeding bird abundance, composition, and diversity. However,
 very few studies directly link measures of bird diversity, composition and
 abundance to measures of forest composition and structure and their
 dynamic change over early succession. This study examines the
 relationships between breeding bird community composition and forest
 structure in regenerating broadleaf forests of southern New England, USA,
 separating the influences of ecological succession from retained stand
 structure. We conducted bird point counts and vegetation surveys across a
 chronosequence of forest stands, that originated between 2 and 24 years
 previously in shelterwood timber harvests, a silvicultural method of
 regenerating oak-mixed broadleaf forests. We distinguish between
 vegetation variables that relate to condition of forest regeneration and
 those that reflect legacy stand structure. Using principal components
 analyses we confirmed the distinction between regeneration and legacy
 vegetation variables. We ran regression analysis to test for relationships
 between bird community variables, including nesting and foraging
 functional guild abundances, and vegetation variables. We confirmed these
 relationships with hierarchical partitioning. Our results demonstrate that
 regenerating and legacy vegetation correlate with bird community variables
 across stand phases, and that the strength with which they drive bird
 community composition changes with forest succession. While measures of
 regeneration condition explain bird abundance and diversity variables
 during late initiation, legacy stand structure explains them during stem
 exclusion. Canopy cover, ground-story diversity, and canopy structure
 diversity are the most powerful and consistent explanatory variables. Our
 results suggest that leaving varied legacy stand structure to promote
 habitat heterogeneity in shelterwood harvests contributes to greater bird
 community diversity. Interestingly, this is particularly important during
 the structurally depauperate phase of stem exclusion of young regenerating
 forests.
DOI: 10.5061/dryad.n8pk0p2rc
title: Messinian vegetation and climate of the intermontane Florina-Ptolemais-Servia Basin, NW Greece: How well do plant fossils reflect past environments?

description: The late Miocene is marked by pronounced environmental changes and the
 appearance of strong temperature and precipitation seasonality. Although
 environmental heterogeneity is to be expected during this time, it is
 challenging to reconstruct palaeoenvironments using plant fossils. We
 investigated leaves and dispersed spores/pollen from 6.4–6 Ma strata in
 the intermontane Florina-Ptolemais-Servia Basin (FPS) of NW Greece. To
 assess how well plant fossils reflect the actual vegetation of the FPS, we
 assigned fossil-taxa to biomes providing a measure for environmental
 heterogeneity. Additionally, the palynological assemblage was compared to
 pollen spectra from modern lake sediments to assess biases in spore/pollen
 representation in the pollen record. We found a close match of the Vegora
 assemblage with modern Fagus–Abies forests of Turkey. Using taxonomic
 affinities of leaf fossils, we further established close similarities of
 the Vegora assemblage with modern laurophyllous oak forests of
 Afghanistan. Finally, using information from sedimentary environment and
 taphonomy, we distinguished local and distantly growing vegetation types.
 We then subjected the plant assemblage of Vegora to different methods of
 climate reconstruction and discussed their potentials and limitations.
 Leaf and spore/pollen records allow accurate reconstructions of
 palaeoenvironments in the FPS, whereas extra-regional vegetation from
 coastal lowlands is likely not captured.
DOI: 10.5061/dryad.gqnk98shj
title: Selection and plasticity both account for inter-annual variation in life-history phenology in an annual prairie legume

description: As the environment changes, so too must plant communities and populations
 if they are to persist. Life-history transitions and their timing are
 often the traits that are most responsive to changing environmental
 conditions. To compare the contributions of plasticity and natural
 selective response to variation in germination and flowering phenology, we
 performed a quantitative genetic study of phenotypic selection on
 Chamaecrista fasciculata (Fabaceae) across two consecutive years in a
 restored tallgrass prairie. The earliest dates of germination and
 flowering were recorded for two parental cohorts and one progeny cohort in
 an experimental garden. Environmental differences between years were the
 largest contributors to phenological variation in this population. In
 addition, there was substantial heritability for flowering time and
 statistically significant selection for advancement of flowering.
 Comparison between a progeny cohort its pre-selection parental cohort
 indicated a change in mean flowering time consistent with the direction of
 selection. Selection on germination time was weaker than that on flowering
 time, while environmental effects on germination time were stronger.
  The response to selection on flowering time was detectable when
 accounting for the effect of the environment on phenotypic differences,
 highlighting the importance of controlling for year-to-year environmental
 variation in quantitative genetic studies.
DOI: 10.5061/dryad.bk3j9kd6w
title: Data from: Link prediction in real-world multiplex networks via layer reconstruction method

description: Networks are invaluable tools to study real biological, social and
 technological complex systems in which connected elements form a
 purposeful phenomenon. A higher resolution image of these systems shows
 that the connection types do not confine to one but to a variety of types.
 Multiplex networks encode this complexity with a set of nodes which are
 connected in different layers via different types of links. A large body
 of research on link prediction problem is devoted to finding missing links
 in single-layer (simplex) networks. In recent years, the problem of link
 prediction in multiplex networks has gained the attention of researchers
 from different scientific communities. Although most of these studies
 suggest that prediction performance can be enhanced by using the
 information contained in different layers of the network, the exact source
 of this enhancement remains obscure. Here, it is shown that similarity
 w.r.t. structural features (eigenvectors) is a major source of
 enhancements for link prediction task in multiplex networks using the
 proposed Layer Reconstruction Method and experiments on real-world
 multiplex networks from different disciplines. Moreover, we characterize
 how low values of similarity w.r.t. structural features result in cases
 where improving prediction performance is substantially hard.
DOI: 10.5061/dryad.dncjsxkvg
title: Paraphyletic species no more – genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)

description: Rapid speciation events, with taxa generated over a short time period, are
 among the most investigated biological phenomena. However, molecular
 systematics often reveals contradictory results compared with
 morphological/phenotypical diagnoses of species under scenarios of recent
 and rapid diversification. In this study, we used molecular data from an
 average of over 29,000 loci per sample from RADseq to reconstruct the
 diversification history and delimit the species boundary in a short-winged
 grasshopper species complex (Melanoplus Scudderi group), where Pleistocene
 diversification has been hypothesized to generate more than 20 putative
 species with distinct male genitalic shapes. We found that based on a
 maximum likelihood molecular phylogeny that each morphological species
 indeed forms a monophyletic group, contrary to the result from a previous
 mitochondrial DNA sequence study. By dating the diversification events,
 the species complex is estimated to have diversified during the Late
 Pleistocene, supporting the recent radiation hypothesis. Furthermore,
 coalescent-based species delimitation analyses provide quantitative
 support for independent genetic lineages, which corresponds with the
 morphologically-defined species. Our results also showed that male
 genitalic shape may not be predicted by evolutionary distance among
 species, indicating that this trait is not only labile, but also implying
 that selection may play a role in character divergence. Additionally, our
 findings suggest that the rapid speciation events in this flightless
 grasshopper complex might be associated primarily with the fragmentation
 of their grassland habitats during the Late Pleistocene. Collectively, our
 study highlights the importance of integrating multiple sources of
 information to delineate species, especially for a species complex that
 diversified rapidly, and whose divergence may be linked to ecological
 processes that create geographic isolation (i.e., fragmented habitats), as
 well as selection acting on characters with direct consequences for
 reproductive isolation (i.e., genitalic divergence).
description: ddRADseq processed data. photo images of
 grasshopper male genitalia. R codes for processing data
 and phylogenetic analyses.
description: Data package includes:  R scripts and input
 data for svdquartets, bpp, and shape analyses
DOI: 10.5061/dryad.fttdz08nz
title: Observation of Sublimation of Ice using Terahertz Spectroscopy

description: Although many studies have investigated the phase change of water, few
 have focused on the sublimation of ice. This study revealed that ice
 sublimation can be observed using terahertz (THz) spectroscopy. Ice was
 observed to undergo sublimation at atmospheric pressure at temperatures
 above 240 K, and its velocity increased in proportion to temperature.
 Above a certain temperature, the absorption coefficient increased during
 sublimation. These findings suggest that an interesting phenomenon may
 occur in the phase change of water at sub-zero temperatures, indicating
 that THz spectroscopy would be useful for measuring water and ice
DOI: 10.5061/dryad.2v6wwpzhk
title: Data from: Implementation of new standard operating procedures for geriatric trauma patients with multiple injuries: a single level I trauma centre study

description: Background The demographic changes towards ageing of the populations in
 developed countries impose a challenge to trauma centres, as geriatric
 trauma patients require specific diagnostic and therapeutic procedures.
 This study investigated whether the integration of new standard operating
 procedures (SOPs) for the resuscitation room (ER) has an impact on the
 clinical course in geriatric patients. The new SOPs were designed for
 severely injured adult trauma patients, based on the Advanced Trauma Life
 Support (ATLS) and imply early whole-body computed tomography (CT), damage
 control surgery, and the use of goal-directed coagulation management.
 Methods Single-centre cohort study. We included all patients ≥ 65
 years of age with an Injury Severity Score (ISS) ≥ 9 who were admitted to
 our hospital primarily via ER. A historic cohort was compared to a cohort
 after the implementation of the new SOPs. Results We enrolled 311 patients
 who met the inclusion criteria between 2000–2006 (group PreSOP) and
 2010–2012 (group SOP). There was a significant reduction in the mortality
 rate after the implementation of the new SOPs (P = .001). This benefit was
 seen only for severely injured patients (ISS ≥ 16), but not for moderately
 injured patients (ISS 9–15). There were no differences with regard to
 infection rates or rate of palliative care. Conclusions We found an
 association between implementation of new ER SOPs, and a lower mortality
 rate in severely injured geriatric trauma patients, whereas moderately
 injured patients did not obtain the same benefit.
DOI: 10.5061/dryad.qjq2bvqc2
title: To hop or not to hop? the answer is in the bird trees

description: Birds can use different types of gaits to move on the ground: they either
 walk, hop, or run. Although velocity can easily explain a preference for
 running, it remains unclear what drives a bird species to favour hopping
 over walking. As many hopping birds are relatively small and arboreal, we
 wanted to test the link between size, arboreality and hopping ability.
 First, we carried out ancestral character state reconstructions of size
 range, hopping ability and ecology on over 1000 species of birds. We found
 that both hopping ability and arboreality were derived and significantly
 correlated traits in avian evolution. Second, we tested the influence of
 hopping ability on the morphology of the lower appendicular skeleton by
 quantifying the shape differences of the pelvis and the three long bones
 of the hind limbs in 47 avian species with different habitats and gait
 preferences. We used geometric morphometrics on 3D landmarks, digitized on
 micro-CT and surface scans of the pelvis, femur, tibiotarsus, and
 tarsometatarsus. Locomotion habits significantly influence the
 conformation of the pelvis, especially at the origin of hip and knee
 muscle extensors. Interestingly, ecology, more than locomotion habits,
 significantly changed tarsometatarsus conformation. The morphology of the
 distal part of the tarsometatarsus constrains digit orientation, which
 leads to a greater ability to perch, an advantageous trait in arboreality.
 The results of this work suggest an arboreal origin of hopping and
 illuminate the evolution of avian terrestrial locomotion.
DOI: 10.5061/dryad.47d7wm38p
title: Data from: Linking dung beetle mediated functions to interactions in the Atlantic Forest: sampling design matters

description: Interactions between dung beetles and vertebrate dung are intimately
 linked to a suite of ecosystem functions in tropical forests. We show that
 the trapping method and the type of dung used affect the suite of beetles
 captured, with the potential to influence the outcome of experiments
 linking functions to interactions.
description: Dung beetle species and abundance attracted to dung baited
 pitfall traps and bag traps from the Atlantic Forest, Brazil. Variation in
 bait type and dung size used as bait recorded.
DOI: 10.5061/dryad.5tb2rbp10
title: Why are there so many flowering plants? A multi-scale analysis of plant diversification

description: The causes of the rapid diversification and extraordinary richness of
 flowering plants (angiosperms) relative to other plant clades is a
 long-standing mystery. Angiosperms are only one among 10 major land plant
 clades (phyla), but include ~90% of land plant species. However, most
 studies that have tried to identify which traits might explain the
 remarkable diversification of angiosperms have focused only on richness
 patterns within angiosperms, and tested only one or a few traits at a
 single hierarchical scale. Here, we assemble a database of 31 diverse
 traits among 678 families and analyze relationships between traits and
 diversification rates across all land plants at three hierarchical levels
 (phylum, order, family) using phylogenetic multiple regression. We find
 that most variation (~85%) in diversification rates among major clades
 (phyla) is explained by biotically mediated fertilization (e.g., insect
 pollination) and clade-level geographic-range size. Different sets of
 traits explain diversification at different hierarchical levels, with
 geographic-range size dominating among families. Surprisingly, we find
 that traits related to local-scale species interactions (i.e. biotic
 fertilization) are particularly important for explaining diversification
 patterns at the deepest timescales, whereas large-scale geographic factors
 (i.e. clade-level range size) are more important at shallower timescales.
 This dichotomy might apply broadly across organisms.
DOI: 10.5061/dryad.qnk98sfbx
title: Ecological fitting is a sufficient driver of tight interactions between sunbirds and ornithophilous plants

description: 1.  Plant-bird pollination interactions evolved independently on
 different continents. Specific adaptations can lead to their restriction
 when potential partners from distant evolutionary trajectories come into
 contact. Alternatively, these interactions can be enabled by convergent
 evolution and subsequent ecological fitting. 2. We studied the
 interactions between New World plants from the genus Heliconia, Asian
 plants of genus Etlingera and African sunbirds on a local farm in
 Cameroon. Heliconia evolved together with hummingbirds and Etlingera spp.
 with spiderhunters - an oriental subgroup of the sunbird family. 
 3. Sunbirds fed on all studied plants and individual plant species were
 visited by a different sunbird spectrum. We experimentally documented a
 higher number of germinated pollen grains in sunbird visited flowers of
 Etlingera spp. For Heliconia spp. this experiment was not successful and
 pollen tubes were rarely observed, even in hand pollinated flowers, where
 enough pollen was deposited. The analyses of contacts with plant
 reproductive organs nevertheless confirmed that sunbirds are good pollen
 vectors for both Heliconia and Etlingera species. 4. Our study
 demonstrated a high ecological fit between actors of distinct evolutionary
 history and the general validity of bird-pollination syndrome. We moreover
 show that trait matching and niche differentiation are important
 ecological processes also in semi-artificial plant-pollinator systems.
description: Dataset contains data about floral morphology, nectar properties
 and sunbird visitation frequences on three <em>Etlingera</em>
 and four <em>Heliconia</em> taxa. Moreover it contains data on
 germination of pollen tubes on these plants when sunbirds were excluded
 (or not) from the pollination systems.
DOI: 10.5061/dryad.m0cfxpnzv
title: Oceanographic drivers of winter habitat use in Cassin's auklets

description: Reduced prey abundance and severe weather can lead to a greater risk of
 mortality for seabirds during the non-breeding winter months. Resource
 patterns in some regions are shifting and becoming more variable in
 relation to past conditions, potentially further impacting survival and
 carryover to the breeding season. As animal tracking technologies and
 methods to analyze movement data have advanced, it has become increasingly
 feasible to draw fine-scale inference about how environmental variation
 affects foraging behavior and habitat use of seabirds during this critical
 period. Here, we used archival light-sensing tags to evaluate how
 inter-annual variation in oceanography affected the winter distribution of
 Cassin’s auklets from Southeast Farallon Island, California. Thirty-five
 out of 93 geolocators deployed from 2015–2017 were recovered and
 successfully recorded light-level data, from which geographic positions
 were estimated. Step-selection functions were applied to identify
 environmental covariates that best explained winter movement decisions and
 habitat use, revealing Cassin’s auklets dispersed farther from the colony
 during a winter with warm SST anomalies, but remained more centralized
 near the breeding colony during two average winters. Movement patterns
 were driven by avoidance of areas with higher sea surface temperatures and
 possible limits of dispersal from the breeding colony, and selection for
 areas with well-defined mesoscale fronts and cooler surface waters.
 Through multiple years of tagging and the application of step-selection
 functions, a robust and widely applied approach for analyzing animal
 movement in terrestrial species, we show how inter-annual differences in
 the movement patterns of a small seabird are driven by oceanographic
 variability across years. Understanding the winter habitat use of seabirds
 can help inform changes in population structure and measures of
 reproductive success, aiding managers in determining potential causes of
 breeding failures.
DOI: 10.5061/dryad.w3r2280m3
title: Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community?

description: Species responses to environmental change are likely to depend on existing
 genetic and phenotypic variation, as well as evolutionary potential. A key
 challenge is to determine whether gene flow might facilitate or impede
 genomic divergence among populations responding to environmental change,
 and if emergent phenotypic variation is limited by gene flow rates. A
 general expectation is that patterns of genetic differentiation in a set
 of co-distributed species reflect differences in dispersal ability. In
 less-dispersive species, we predict greater genetic divergence and reduced
 gene flow. This could lead to covariation in life-history traits due to
 local adaptation, although plasticity or drift could mirror these
 patterns. Here we compare genome-wide patterns of genetic structure in
 four phenotypically variable grasshopper species along a steep elevation
 gradient near Boulder, Colorado. We test the hypothesis that genomic
 differentiation is greater in short-winged grasshopper species, and
 statistically associated with variation in growth, reproductive and
 physiological traits along the elevational gradient. In addition, we
 estimate rates of gene flow under competing demographic models, as well as
 potential gene flow through surveys of phenological overlap among
 populations within a species. All species exhibit genetic structure along
 the elevation gradient and limited gene flow. The most pronounced genetic
 divergence appears in short-winged (less-dispersive) species, which also
 exhibit less phenological overlap among populations. A high elevation
 population of the most widespread species, Melanoplus sanguinipes, appears
 to be a sink population derived from low elevation populations. While
 dispersal ability has a clear connection to the genetic structure in
 different species, genetic distance does not predict growth, reproductive
 or physiological trait variation in any species, and evidence for local
 adaptation in these species remains equivocal.
description: The dataset includes additional figures for genetic analysis of
 four grasshopper species, as well as supporting data and files for
 conducting ABC analysis of gene flow.
description: Supplemental File 1 (.docx file): Provides figures and tables
 related to genetic analysis of population structure, and ABC modeling of
 gene flow. Supplemental File 2 (.xlsx file): The
 barcode, sample identifier and population identifier for demultiplexing
 Illumina short read data (NCBI Bioproject PRJNA547722).
 Supplemental File 3 (zip archive of text files): Input files to
 conduct fastsimcoal simulations. Supplemental File 4
 (zip archive of text files): Custom R scripts for population genetics data
 analysius.