cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.69gt3
title: Data from: Precipitation and environmental constraints on three aspects of flowering in three dominant tallgrass species

description: Flower production can comprise up to 70% of aboveground primary production
 in grasslands. Yet we know relatively little about how the environment and
 timing of rainfall determine flower productivity. Evidence suggests that
 deficits or additions of rainfall during phenlologically relevant periods
 (i.e. growth, storage, initiation of flowering, and reproduction) can
 determine flower production in grasslands. We used long-term data from the
 Konza Prairie LTER to test how fire, soil topography, and precipitation
 amounts during four phenologically relevant periods of the growing season
 constrain three aspects of flowering in three dominant C4 grass species.
 Specifically, we examined the probability of flowering, flowering stalk
 density, and individual flowering stalk biomass for Andropogon gerardii,
 Schizachyrium scoparium and Sorghastrum nutans. We found that each of the
 three species responded to the amount of precipitation during
 phenologically relevant periods in unique ways. All aspects of A. gerardii
 flowering were sensitive to precipitation during the flowering stalk
 elongation period (June 20 – Aug 3). The probability of S. nutans
 flowering was partly determined by precipitation during the rapid growth
 phase (April 21 – June 4), whereas flowering stalk density of this species
 depended on rainfall during flowering stalk elongation (June 20 – Aug 3).
 In contrast, all aspects of flowering of S. scoparium were relatively
 independent of rainfall during any period. Our results demonstrate that
 three functionally similar, codominant C4 grass species respond
 differently to phenologically relevant precipitation periods. As a result,
 drought during any phenological window during the growing season can
 adversely impact biomass and flowering production of grasslands via
 species-specific reductions in flowering stalk density and biomass.
description: PRE021This file contains
 flowering stem height for all transect/watershed/year combinations at
 Konza Prairie used in this study.PRE022This file contains the
 weight of flowering stalk biomass for all transect/watershed/year
 combinations at Konza Prairie used in this study.pre022.15.csvClimDBRainFallDaily precipitation estimates for Konza Prairie LTER site as recorded by the ClimDB database.KFH011Burn history for Konza Prairie watersheds.Processing ScriptR script for processing flower data into the final datasheet that contains the stalk weight, stalk height, and burn history for all transect/watershed/year combinations in this study.Flower.RMetadataMetadata file that includes column descriptions and associated data sources for all data in the final analysis file as processed by the Processing R script.Flower_Metadata.txt
DOI: 10.5061/dryad.rd748
title: Data from: DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)

description: The analysis of apex predator diet has the ability to deliver valuable
 insights into ecosystem health, and the potential impacts a predator might
 have on commercially relevant species. The Australian sea lion (Neophoca
 cinerea) is an endemic apex predator and one of the world's most
 endangered pinnipeds. Given that prey availability is vital to the
 survival of top predators, this study set out to understand what dietary
 information DNA metabarcoding could yield from 36 sea lion scats collected
 across 1,500 km of its distribution in southwest Western Australia. A
 combination of PCR assays were designed to target a variety of potential
 sea lion prey, including mammals, fish, crustaceans, cephalopods, and
 birds. Over 1.2 million metabarcodes identified six classes from three
 phyla, together representing over 80 taxa. The results confirm that the
 Australian sea lion is a wide-ranging opportunistic predator that consumes
 an array of mainly demersal fauna. Further, the important commercial
 species Sepioteuthis australis (southern calamari squid) and Panulirus
 cygnus (western rock lobster) were detected, but were present in
 &lt;25% of samples. Some of the taxa identified, such as fish, sharks
 and rays, clarify previous knowledge of sea lion prey, and some, such as
 eel taxa and two gastropod species, represent new dietary insights. Even
 with modest sample sizes, a spatial analysis of taxa and operational
 taxonomic units found within the scat shows significant differences in
 diet between many of the sample locations and identifies the primary taxa
 that are driving this variance. This study provides new insights into the
 diet of this endangered predator and confirms the efficacy of DNA
 metabarcoding of scat as a noninvasive tool to more broadly define
 regional biodiversity.
description: DNA metabarcoding for
 diet analysis and biodiversity A case study using the endangered
 Australian sea lionResults from a dietary
 study. The file contains mostly unique filtered fasta files of DNA
 sequences extracted and amplified from the scat of the Australian Sea Lion
 (Neophoca cinerea). The assays used focused mainly on fish, crustaceans,
 and cephalopods.
DOI: 10.5061/dryad.4j1qt
title: Data from: Multiple sequence alignment averaging improves phylogeny reconstruction

description: The classic methodology of inferring a phylogenetic tree from sequence
 data is composed of two steps. First, a multiple sequence alignment (MSA)
 is computed. Then, a tree is reconstructed assuming the MSA is correct.
 Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce
 tree inference accuracy. It was previously proposed that filtering
 unreliable alignment regions can increase the accuracy of tree inference.
 However, it was also demonstrated that the benefit of this filtering is
 often obscured by the resulting loss of phylogenetic signal. In this work
 we explore an approach, in which instead of relying on a single MSA, we
 generate a large set of alternative MSAs and concatenate them into a
 single SuperMSA. By doing so, we account for phylogenetic signals
 contained in columns that are not present in the single MSA computed by
 alignment algorithms. Using simulations, we demonstrate that this approach
 results, on average, in more accurate trees compared to (1) using an
 unfiltered MSA; (2) using a single MSA with weights assigned to columns
 according to their reliability. Next, we explore in which regions of the
 MSA space our approach is expected to be beneficial. Finally, we provide a
 simple criterion for deciding whether or not the extra effort of computing
 a SuperMSA and inferring a tree from it is beneficial. Based on these
 assessments, we expect our methodology to be useful for many cases in
 which diverged sequences are analyzed. The option to generate such a
 SuperMSA is available at http://guidance.tau.ac.il
description: ENSEMBLsim_datasetThe ENSEMBLsim simulated dataset examined in this study.SuppMaterial_SuperMSASupplementary figures, tables, and text
DOI: 10.5061/dryad.p2s02
title: Data from: Sanctions, partner recognition, and variation in mutualism

description: Mutualistic interactions can be stabilized against invasion by
 noncooperative individuals by putting such “cheaters” at a selective
 disadvantage. Selection against cheaters should eliminate genetic
 variation in partner quality—yet such variation is often found in natural
 populations. One explanation for this paradox is that mutualism outcomes
 are determined not only by responses to partner performance but also by
 partner signals. Here, we build a model of coevolution in a symbiotic
 mutualism, in which hosts’ ability to sanction noncooperative symbionts
 and recognition of symbiont signals are determined by separate loci, as
 are symbionts’ cooperation and expression of signals. In the model,
 variation persists without destabilizing the interaction, in part because
 coevolution of symbiont signals and host recognition is altered by the
 coevolution of sanctions and cooperation, and vice versa. Individual-based
 simulations incorporating population structure strongly corroborate these
 results. The dual systems of sanctions and partner recognition converge
 toward conditions similar to some economic models of mutualistic
 symbiosis, in which hosts offering the right incentives to potential
 symbionts can initiate symbiosis without screening for partner quality.
 These results predict that mutualists can maintain variation in
 recognition of partner signals or in the ability to sanction
 noncooperators without destabilizing mutualism, and they reinforce the
 notion that studies of mutualism should consider communication between
 partners as well as the exchange of benefits.
description: Analytic derivations,
 simulation code, and simulation resultsThe ZIP archive contains
 derivations of the analytic models, as both Mathematica notebooks and PDF
 documents, R scripts for individual-based simulations, and output from
 simulations reported in the paper. See the README for more
 detail.for_dryad.zip
DOI: 10.5061/dryad.j1h2v
title: Data from: Collision sensitive niche profile of the worst affected bird-groups at wind turbine structures in the federal state of Brandenburg, Germany

description: Biodiversity-related impacts at wind energy facilities have increasingly
 become a cause of conservation concern, central issue being the collision
 of birds. Utilizing spatial information of their carcass detections at
 wind turbines (WTs), we quantified the detections in relation to the
 metric distances of the respective turbines to different land-use types.
 We used ecological niche factor analysis (ENFA) to identify combinations
 of land-use distances with respect to the spatial allocation of WTs that
 led to higher proportions of collisions among the worst affected
 bird-groups: Buntings, Crows, Larks, Pigeons and Raptors. We also assessed
 their respective similarities to the collision phenomenon by checking for
 overlaps amongst their distance combinations. Crows and Larks showed the
 narrowest “collision sensitive niche”; a part of ecological niche under
 higher risk of collisions with turbines, followed by that of Buntings and
 Pigeons. Raptors had the broadest niche showing significant overlaps with
 the collision sensitive niches of the other groups. This can probably be
 attributed to their larger home range combined with their hunting
 affinities to open landscapes. Identification of collision sensitive
 niches could be a powerful tool for landscape planning; helping avoid
 regions with higher risks of collisions for turbine allocations and thus
 protecting sensitive bird populations.
description: Bird
 GroupsCoordinatesBird_Groups.zipDistance FilesASCII filesDistance_Files.zip
DOI: 10.17632/s6mvxmxpr7
title: TrEsqCarn
DOI: 10.17632/s6mvxmxpr7.1
title: TrEsqCarn
DOI: 10.5061/dryad.412nn
title: Data from: A synthesis of diets and trophic overlap of marine species in the California current

description: A key step toward ecosystem-based management is to better understand how
 interactions within food webs affect species of commercial and
 conservation importance. Here we provide comprehensive diet information
 and food web analysis for major taxa within the California Current
 ecosystem, including fish, marine mammals, birds, and invertebrates. We
 synthesized 75 published diet studies from this ecosystem and calculated
 representative diets for each species or aggregated functional group. We
 assessed diet relatedness using hierarchical cluster analysis and
 calculated diet overlaps based on percent similarity index (PSI). Both
 analyses were performed on functional group data and also separately for
 each vertebrate species. Cluster analysis identified distinct feeding
 guilds and revealed both intuitive and novel diet similarities between
 several species and functional groups. One intuitive example is that
 functional groups preying on euphausiids, a key forage species in the
 California Current, show a high amount of overlap. A novel example is the
 significant diet overlap of shallow small rockfish and baleen whales
 (e.g., grey whales [Eschrichtius robustus]), both of which consume large
 amounts of benthic invertebrates. Functional groups were highly
 significant in explaining the PSI differences between species, which
 suggests that key ecological interactions will be preserved in ecosystem
 models that use these functional groups. A visual representation of the
 complete food web and calculation of food web statistics suggest that
 there are strong similarities between the food webs of the California
 Current and the Benguela Current, a similar upwelling-driven eastern
 boundary current off the southwest coast of Africa.
description: DietsOfPredatorsThatAreJuvenilesDiets of California Current marine animals (West Coast of US, parts of Canada and Mexico) for predators that are juveniles.DietsOfPredatorsThatAreAdultsOrLackAgeStructureDiets of California Current (West Coast of US, parts of Canada and Mexico) for predators that are either Adults or invertebrates that lack age structure.DietMatrixWippelUpdated_CaliforniaCurrentDietMatrixWippelUpdated_CaliforniaCurrent.xlsx This is a Microsoft Excel 2016 spreadsheet. This is the complete collection of diet information. See NOTES page and the full README file.
DOI: 10.5061/dryad.s4f13
title: Data from: Reflectance confocal microscopy features of BRAF V600E mutated thin melanomas detected by immunohistochemistry

description: The classification of melanoma into four histological subtypes has been
 questioned regarding its clinical validity in providing relevant
 information for treatment for metastatic tumors. Specific genetic
 alterations are associated with particular clinical and histopathological
 features, suggesting that these could be helpful in refining existing
 melanoma classification schemes. We analyzed BRAF V600E mutated melanomas
 to explore the Reflectance confocal microscopy (RCM) utility as a
 screening aid in the evaluation of the most appropriate patients for
 genetic testing. Thus, 32 melanomas were assessed regarding their BRAF
 V600E mutational status. Experts blinded to dermoscopic images and V600E
 immunohistochemistry results evaluated RCM images regarding previously
 described melanoma features. BRAF positive melanomas were related to
 younger age (p=0.035), invasive melanomas (p=0.03) and to the presence of
 hiporreflective cells (p=0.02), epidermal nests (p=0.02), dermal-epidermal
 junction nests (p=0.05), edged papillae (p=0.05), and bright dots
 (p=0.05), and to absence of junctional thickening due to isolated cells
 (p=0.01) and meshwork (p=0.02). This study can not characterize other
 mutations in the BRAF, because the immunohistochemistry is specific to the
 type V600E. The findings should encourage the genetic evaluation of BRAF
 mutation. This study highlights the potential of RCM as a supplementary
 tool in the screening of BRAF-mutated melanomas.
description: Reflectance confocal
 microscopy features of BRAF V600E mutated thin melanomas detected by
 immunohistochemistry dataData in excel sheet used
 in the article: Reflectance confocal microscopy features of BRAF V600E
 mutated thin melanomas detected by immunohistochemistryUAC_ PONE-D-17-07514_RCM of
 BRAF V600E mutated thin melanomas detected IHQ
 data.xlsUAC_Tables 1 to
 7_PONE-D-17-07514_RCM of BRAF V600E mutated thin melanomas detected
 IHQAll tables (1 to 7) in
 the article Reflectance confocal microscopy features of BRAF V600E mutated
 thin melanomas detected by immunohistochemistryTables 1 to
 7.docUAC_PONE-D-17-07514_RCM
 of BRAF V600E mutated thin melanomas detected IHQ statistical
 analysesStatistical analysis of
 data presented in the paper Reflectance confocal microscopy features of
 BRAF V600E mutated thin melanomas detected by
 immunohistochemistry
DOI: 10.5061/dryad.4588p
title: Data from: Dispersal in dendritic networks: ecological consequences on the spatial distribution of population densities

description: 1. Understanding the consequences of spatial structure on ecological
 dynamics is a central theme in ecology. Recently, research has recognized
 the relevance of river and river-analogue network structures, because
 these systems are not only highly diverse but also rapidly changing due to
 habitat modifications or species invasions. 2. Much of the previous work
 on ecological and evolutionary dynamics in metapopulations and
 metacommunities in dendritic river networks has been either using
 comparative approaches or was purely theoretical. However, the use of
 microcosm experiments provides the unique opportunity to study large-scale
 questions in a causal and experimental framework. 3. We conducted
 replicated microcosm experiments, in which we manipulated the spatially
 explicit network configuration of a landscape and addressed how linear
 versus dendritic connectivity affects population dynamics, specifically
 the spatial distribution of population densities, and movement behavior of
 the protist model organism Tetrahymena pyriformis. We tracked population
 densities and individual-level movement behavior of thousands of
 individuals over time. 4. At the end of the experiment, we found more
 variable population densities between patches in dendritic networks
 compared to linear networks, as predicted by theory. Specifically, in
 dendritic networks, population densities were higher at nodes that
 connected to headwaters compared to the headwaters themselves and to more
 central nodes in the network. These differences follow theoretical
 predictions and emerged from the different network topologies per se.
 These differences in population densities emerged despite weakly
 density-dependent movement. 5. We show that differences in network
 structure alone can cause characteristic spatial variation in population
 densities. While such differences have been postulated by theoretical work
 and are the underlying precondition for differential dispersal evolution
 in heterogeneous networks, our results may be the first experimental
 demonstration thereof. Furthermore, these population-level dynamics may
 affect extinction risks and can upscale to previously shown metacommunity
 level diversity dynamics. Given that many species in natural river systems
 exhibit strong spatio-temporal patterns in population densities, our work
 suggests that abundance patterns should not only be addressed from a local
 environmental perspective, but may be the outcome of processes that are
 inherently driven by the respective habitat network structure.
description: data
DOI: 10.5061/dryad.1464
title: Data from: Distorted views of biodiversity: spatial and temporal bias in species occurrence data

description: Historical as well as current data on species distributions are needed to
 track changes in biodiversity. Species distribution data are found in a
 variety of sources but is likely that they include different biases
 towards certain time periods or places. By collating a large historical
 database of ~170,000 records of species in the avian order Galliformes
 dating back over two centuries and covering Europe and Asia, we
 investigate patterns of spatial and temporal bias in five sources of
 species distribution data; museum collections, the scientific literature,
 ringing records, ornithological atlases and website reports from ‘citizen
 scientists’. Museum data were found to provide the most comprehensive
 historical coverage of species’ ranges but often proved extremely
 time-expensive to collect. Literature records have increased in their
 number and coverage through time whereas ringing, atlas and website data
 are almost exclusively restricted to the last few decades. Geographically,
 our data were biased towards Western Europe and Southeast Asia. Museums
 were the only data source to provide reasonably even spatial coverage
 across the entire study region. In the last three decades, literature data
 have become increasingly focussed towards threatened species and protected
 areas and currently no source is providing reliable baseline information,
 a role once filled by museum collections. As well as securing historical
 data for the future, and making it available for users, the sampling
 biases will need to be understood and addressed if we are to obtain a true
 picture of biodiversity change.
description: GALLIFORM: WPA Eurasian
 Database v 1.0.Records refer to species
 occurrence data collected from museum collections, the literature,
 ornithological atlases, bird ringing programmes or ornithological trip
 report websites. Records which could be at least approximately dated and
 georeferenced are contained in a comma delimited text file. The file gives
 information on the data source, the year of the record, the species the
 record relates to, the threat status of the species, the country the
 record is from and whether the record came from inside a protected area.
 The column names are mostly self-explanatory. In cases where an exact year
 of record was not known, a date range is given. For example, ‘Pre 1980’
 would indicate a record from 1979 or earlier. Similarly, ‘Post 1980’ would
 indicate a record from 1981 or later. For the column ‘Threatened?’, ‘0’
 indicates a non-threatened species and ‘1’ a threatened species. For the
 column ‘Inside a Protected Area?’ ‘0’ indicates the record is from outside
 a protected area and ‘1’ inside a protected area.BoakesEtAlDatasetS1.txt
DOI: 10.5061/dryad.5br8k
title: Data from: Body shape convergence driven by small size optimum in marine angelfishes

description: Convergent evolution of small body size occurs across many vertebrate
 clades and may reflect an evolutionary response to shared selective
 pressures. However it remains unclear if other aspects of phenotype
 undergo convergent evolution in miniaturized lineages. Here we present a
 comparative analysis of body size and shape evolution in marine
 angelfishes (Pomacanthidae), a reef fish family characterized by repeated
 transitions to small body size. We ask if lineages that evolve small sizes
 show convergent evolution in body shape. Our results reveal that angelfish
 lineages evolved three different stable size optima with one corresponding
 to the group of pygmy angelfishes (Centropyge). Then, we test if the
 observed shifts in body size are associated with changes to new adaptive
 peaks in shape. Our data suggest that independent evolution to small size
 optima have induced repeated convergence upon deeper body and steeper head
 profile in Centropyge. These traits may favour manoeuvrability and visual
 awareness in these cryptic species living among corals, illustrating that
 functional demands on small size may be related to habitat specialization
 and predator avoidance. The absence of shape convergence in large marine
 angelfishes also suggests that more severe requirements exist for small
 than for large size optima.
description: FREDERICH_Angelfishes_specimen_List_TableS1Table S1. List of studied species and their maximum total length (TL). The number of used X-rays (n) and the Genbank accession numbers are also provided.FREDERICH_Appendices_Figures_ESMA single pdf file including the Appendices S1-S3 and the Figures S1-S4.