cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t53g6p1
title: Data from: Interspecific covariation in courtship displays, iridescent plumage, solar orientation, and their interactions in hummingbirds

description: Many animals communicate using multiple signals. Historically, most
 attention was paid to how these traits evolve and function in isolation,
 but recent work has focused on how signals may interact with one another
 and produce unique signal interaction properties. These interaction
 properties vary within species, but little is known about how they vary
 among species, especially with regards to how the expression of particular
 signals may drive different signal interaction mechanisms. We studied the
 evolutionary relationships between iridescent plumage, courtship (shuttle)
 displays, solar environment, and male color appearance during a display
 (i.e. the signal interaction property) among six species of North American
 “bee” hummingbirds. We found that color appearances co-vary with
 behavioral and plumage properties, which themselves negatively co-vary,
 such that species with more exaggerated displays appeared flashier during
 courtship, while species with more exaggerated plumage appeared
 brighter/more colorful with minimal color-changes. By understanding how
 signal interaction properties co-vary with signals, we were able to
 discover the complex, multi-layered evolutionary relationships underlying
 these traits and uncover new potential drivers of signal evolution. Our
 results highlight how studying the interaction properties between animal
 signals provides a richer understanding of how those traits evolved and
 diversified.
description: Bee_hummingbird_data_RKSBee_hummingbird_data_RKS is an excel sheet with two tabs of data. The first tab - individual_data - contains information about the id/species, morphology, display characteristics, plumage patch size, feather reflectance, and display environment for each bee hummingbird male in this study. The second tab - display-color_data - contains information about each male's individual displays; specifically the angular distances he moved, the angles at which he oriented himself relative to the female, and the photometric variables (luminance, UV cone stimulation, SW cone stimulation, MW cone stimulation, and LW cone stimulation).
DOI: 10.5061/dryad.73pn293
title: Data from: Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae)

description: Gene flow via pollen movement affects genetic variation in plant
 populations and is an important consideration in plant domestication.
 Fontainea picrosperma is a subcanopy rainforest tree that is of commercial
 interest because it is the source of tigilanol tiglate, a natural product
 used for the treatment of solid tumors. We identify patterns of
 pollen-mediated gene flow within natural populations of F. picrosperma and
 estimate genetic parameters and genetic structure between adult and
 juvenile groups using microsatellite markers. Our results show pollination
 events occur over much shorter distances than reported for tropical canopy
 species. At least 63 % of seeds are sired by male trees located within 30
 m of the mother. On average, 27 % of the local male population contributed
 to successful reproduction of F. picrosperma with most fathers siring a
 single seed, however, the contributions to reproduction were uneven.
 Larger male trees with more flowers had gre ater reproductive success than
 those with less flowers (P &lt; 0.05). There were comparatively low
 levels of genetic variation across the species (HE = 0.405 for adult trees
 and 0.379 for juveniles) and we found no loss of genetic diversity between
 adult and juvenile trees. Short distance pollen flow and low genetic
 diversity is theoretically a prelude to genetic impoverishment, however F.
 picrosperma has persisted through multiple significant climatic
 oscillations. Nevertheless, the remaining low genetic diversity is of
 concern for domestication programs which require maximal genetic diversity
 to facilitate efficient selective breeding and genetic improvement of this
 commercially significant species.
description: Allele report_Paternity
 study F. picrospermaAllele reports of the
 samples used in the CERVUS analysis of the subpopulation paternity
 analysis of mother trees and the respective germinated
 seedlingsMale fitness
 parameters_Paternity Study F. picrospermaData used in the
 putative father fitness analysis to determine factors of reproductive
 success. Variables include: distance, direction, size and flowering effort
 of the male trees surrounding the focal mother tree.Allele report_Genetic
 diversity and differentiation in F. picrosperma adults and
 juvenilesAllele reports of the
 samples used in the genetic diversity and differentiation study of adult
 and juvenile trees.
DOI: 10.5061/dryad.t1s010m
title: Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

description: Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N
 to ecosystems, but only if they are sufficiently abundant. The overall
 abundance and latitudinal abundance distributions of N‐fixing trees are
 well characterised in the Americas, but less well outside the Americas.
 Here, we characterised the abundance of N‐fixing trees in a network of
 forest plots spanning five continents, ~5,000 tree species and ~4 million
 trees. The majority of the plots (86%) were in America or Asia. In
 addition, we examined whether the observed pattern of abundance of
 N‐fixing trees was correlated with mean annual temperature and
 precipitation. Outside the tropics, N‐fixing trees were consistently rare
 in the forest plots we examined. Within the tropics, N‐fixing trees were
 abundant in American but not Asian forest plots (~7% versus ~1% of basal
 area and stems). This disparity was not explained by mean annual
 temperature or precipitation. Our finding of low N‐fixing tree abundance
 in the Asian tropics casts some doubt on recent high estimates of N
 fixation rates in this region, which do not account for disparities in
 N‐fixing tree abundance between the Asian and American tropics. Synthesis.
 Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which
 is constrained by the abundance of N‐fixing trees. By analysing a large
 dataset of ~4 million trees, we found that N‐fixing trees were
 consistently rare in the Asian tropics as well as across higher latitudes
 in Asia, America and Europe. The rarity of N‐fixing trees in the Asian
 tropics compared with the American tropics might stem from lower intrinsic
 N limitation in Asian tropical forests, although direct support for any
 mechanism is lacking. The paucity of N‐fixing trees throughout Asian
 forests suggests that N inputs to the Asian tropics might be lower than
 previously thought.
description: MengeEtAl_Appendix1_SuppInfo_FinalThis includes further details of the statistical analyses used, together with additional figures (Figures S1 to S13) and an additional table (Table S1).MengeEtAl_Appendix2_SuppInfo_FinalThis is a spreadsheet showing key data used in the statistical analyses presented.
DOI: 10.5061/dryad.gf52g00
title: Data from: The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives

description: Here, we report the draft genome sequence of Solanum commersonii, which
 consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12
 chromosomes, using the potato (Solanum tuberosum) genome sequence as a
 reference. Compared with potato, S. commersonii shows a striking reduction
 in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes
 were mainly due to variations in intergenic sequence length. Gene
 annotation by ab initio prediction supported by RNA-seq data produced a
 catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which
 20% are shown to target cold-responsive genes, and 39,290 protein-coding
 genes with a significant repertoire of nonredundant nucleotide binding
 site-encoding genes and 126 cold-related genes that are lacking in S.
 tuberosum. Phylogenetic analyses indicate that domesticated potato and S.
 commersonii lineages diverged ∼2.3 million years ago. Three duplication
 periods corresponding to genome enrichment for particular gene families
 related to response to salt stress, water transport, growth, and defense
 response were discovered. The draft genome sequence of S. commersonii
 substantially increases our understanding of the domesticated germplasm,
 facilitating translation of acquired knowledge into advances in crop
 stability in light of global climate and environmental changes.
description: S_commersoni.genome_underscore.1000bp.listGenome assembly of S. commersonii, containing 63,630 scaffold sequencesproteins.faProtein sequences of genes in S. commersoniifiltered_proteins.fastafiltered_final_okGeneric feature format file (gff) of genes in S. commersoniifiltered_transcriptsTranscript sequences (cDNA) of genes in S. commersoniiRNAseq_tissues_genesExpression abundance of representative gene models in four tissues (flowers, leaves, roots and tubers)Functional annotationFunctional annotation of working gene model set in S. commersoniifiltered.annotfiltered_microRNAGeneric feature format file (gff3) of microRNAs in S. commersoniimicro_finalSequences of microRNA identified in S. commersoniitarget genes of microRNAsSequences of target microRNAs identified in S. commersoniitargetmicro.fafiltered_microRNA_precursorGeneric feature format file (gff3) of precursor of microRNAs in S. commersonii
DOI: 10.5061/dryad.7nf7d35
title: Data from: Modified HEPES one-pot synthetic strategy for gold nanostars

description: Gold nanostars are being utilized more regularly in the biosensing field.
 Despite their useful attributes, there is still a need to optimize aspects
 of the synthesis and stability. The seedless, synthetic method comprised
 of 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) is a facile,
 rapid method, however, produces heteromorphic nanostars. The modification
 of a HEPES method resulted in a silver-assisted, seedless gold nanostar
 synthesis method. The nanostars resulting from this method were
 monodispersed, multi-branched and approximately 37nm + 2nm in diameter. It
 proved to be a repeatable method that produced homogenous and robust
 nanostars. Once functionalized with polyvinylpyrrolidone 10 000, the new
 nanostars were observed to be stable in various environments such as salt,
 ionic strength and cell culture medium. In conclusion, the addition of the
 silver nitrate improved the morphology of the reported HEPES nanostars for
 the purpose of nanobiosensor development.
description: Au+ and Au- stability
 dataThis data is for
 nanoparticle stability in various conditions afters 24
 hoursAUANDA~1.XLSIncreased silver concentrationSpectra for the synthesis of the nanostars with the increase of silver nitrate concentrationEXPERI~1.XLS
DOI: 10.5281/zenodo.18146546
title: Scaned grapevine leaves from Balearic Islands, Spain
DOI: 10.5281/zenodo.18146547
title: Scaned grapevine leaves from Balearic Islands, Spain
DOI: 10.15468/dl.7r7kvr
title: Occurrence Download

description: A dataset containing 415 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ateles chamek"
 ]
}

 The dataset includes 415 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001683-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.59p3vv5
title: Data from: Biodiversity and thermal ecological function: the influence of freshwater algal diversity on local thermal environments

description: The influence of temperature on diversity and ecosystem functioning is
 well studied; the converse however, i.e. how biodiversity influences
 temperature, much less so. We manipulated freshwater algal species
 diversity in microbial microcosms to uncover how diversity influenced
 primary production, which is well documented in biodiversity research. We
 then also explored how visible-spectrum absorbance and the local thermal
 environment responded to biodiversity change. Variations in the local
 thermal environment, that is, in the temperature of the immediate
 surroundings of a community, are known to matter not only for the rate of
 ecosystem processes, but also for persistence of species assemblages and
 the very relationship between biodiversity and ecosystem functioning. In
 our microcosm experiment, we found a significant positive association
 between algal species richness and primary production, a negative
 association between primary production and visible-spectrum absorbance,
 and a positive association between visible-spectrum absorbance and the
 response of the local thermal environment (i.e., change in thermal
 infrared emittance over a unit time). These findings support an indirect
 effect of algal diversity on the local thermal environment pointing to a
 hitherto unrecognized biodiversity effect in which diversity has a
 predictable influence on local thermal environments.
description: Microcosm experiment
 dataFile contains
 experimental data from the microcosm experiment, namely: flask ID, author
 initials, date, initial microcosm richness (species), initial microcosm
 richness (groups), presence dummies for all 8 species, total biovolume,
 cell counts for each of the 5 groups, temperature before exposure (TB),
 minimum, maximum, standard deviation (sd) of TB within Petri dish, time of
 measurement of TB, temperature after exposure to light (TA), minimum,
 maximum, sd of TA, time of measure of TA, temperature difference (TA-TB),
 mean, sd, minimum, maximum RGB, "second batch" dummy, time trend
 for the first batch, time (in hours, minutes), time trend of the second
 batch, dummy for the presence of the IG (isomorphic group),
 complementarity and sampling effects (and intermediary calculations)
 within each microcosm. Volumes are in 10e-6 m3, temperatures in
 °C.algaeData.csv
DOI: 10.5061/dryad.39121ns
title: Data from: Benthic community history in the Changjiang (Yangtze River) mega delta: Damming, urbanization, and environmental control

description: Coastal environment of the Changjiang delta has been influenced by recent
 anthropogenic activities such as dam constructions, and increased sewage
 and fertilizer inputs. Previous work examined compositional shift of
 marine plankton to assess ecological impacts of these activities on marine
 ecosystems in the Changjiang discharge area. Here we used benthic marine
 ostracodes collected in the Changjiang Estuary and its adjacent East China
 Sea in the 1980s and the 2010s, respectively, to investigate temporal
 changes of the benthic community and the controlling factors of the
 benthic fauna. Our results revealed more shoreward distribution of some
 well-known off-shore ostracode species in the 2010s compared to the 1980s,
 and relatively more important role of environmental processes (e.g. bottom
 water temperature, bottom water salinity and the eutrophic conditions of
 surface water) than spatial processes (e.g. the flow of ocean currents) in
 structuring ostracode compositions. The temporal changes of ostracode
 community were likely attributed to the combined effects of reduced
 seasonal water and sediment discharge, and eutrophic conditions of the
 Changjiang due to numerous dam constructions along the Changjiang and
 population expansion in the Changjiang basin. Results of redundancy
 analysis and variation partitioning suggested that ocean currents
 facilitated environmental filtering of ostracode species such that they
 could disperse to preferred environmental conditions. These findings
 highlighted the potential uses of marine microfossils to better understand
 ecological impacts on benthic ecosystem in vulnerable Asian mega deltas
 and provided insights into the integration of metacommunity concepts in
 disentangling dynamics of marine benthic communities.
description: CheungetlSupplementary
 ostracod and environmental dataTable S1 Ostracode
 dataset for figures 4-6; Table S2 Ostracode dataset of sampling locations
 used in RDA Table S3 Environmental data of sampling locations used in
 RDA
DOI: 10.5061/dryad.q5846sq
title: Data from: Head shape modulates diversification of a classic cichlid pharyngeal jaw innovation

description: Functional innovations are often invoked to explain the uneven
 distribution of ecological diversity. Innovations may provide access to
 new adaptive zones by expanding available ecological opportunities and may
 serve as catalysts of adaptive radiation. However, diversity is often
 unevenly distributed within clades that share a key innovation,
 highlighting the possibility that the impact of the innovation is mediated
 by other traits. Pharyngognathy is a widely recognized innovation of the
 pharyngeal jaws that enhances the ability to process hard and tough prey
 in several major radiations of fishes, including marine wrasses and
 freshwater cichlids. We explored diversification of lower pharyngeal jaw
 shape, a key feature of pharyngognathy, and the extent to which it is
 influenced by head shape in Neotropical cichlids. While pharyngeal jaw
 shape was unaffected by either head length or head depth, its disparity
 declined dramatically with increasing head width. Head width also
 predicted the rate of pharyngeal jaw evolution such that higher rates were
 associated with narrow heads. Wide heads are associated with exploiting
 prey that require intense processing by pharyngeal jaws that have expanded
 surfaces for the attachment of enlarged muscles. However, we show that a
 wide head constrains access to adaptive peaks associated with several
 trophic roles. A constraint on the independent evolution of pharyngeal jaw
 and head shape may explain the uneven distribution of ecological diversity
 within a clade that shares a major functional innovation.
description: Accession numbers and
 morphological dataThis file contains the
 accession numbers of the specimens used in the study as well as the
 underlying morphological data used in the analyses.Accession_numbers_and_morphological_data.pdftrees file n100This file contains 100 phylogenetic trees that were used in the study.trees_file_n100.tree
DOI: 10.5061/dryad.1g1hh58
title: Data from: Seasonal contrasts in individual consistency of oriental honey buzzards’ migration

description: Individual consistency in migration can shine light on the mechanisms of
 migration. Most studies reported that birds are more consistent in the
 timing than in the routes or stopover sites during migration, but some
 specialist species showed the opposite patterns, being more consistent in
 spatial than temporal aspects of migration. One possible explanation for
 this contrast is that specialists rely on particular food or habitat
 resources, which restrict the migratory routes they can take, leading to
 high spatial consistency. If this is the case, the effect of specialist
 foraging should become apparent only when birds forage, instead of fasting
 and flying continuously. To test this effect, we analysed individual
 consistency in migration of the oriental honey buzzard (Pernis
 ptilorhynchus), a specialist raptor that feeds on honeybees and wasps,
 using a long-term tracking data set. As honey buzzards make extended
 stopovers during which they forage in spring but not in autumn, the
 spatial consistency should be higher in spring than in autumn. Honey
 buzzards were highly consistent in both their migratory routes and
 stopover sites in Southeast Asia, but only during spring migration. Our
 results highlight an important link between species’ migratory consistency
 and foraging ecology.
description: Latitude crossing data
 of oriental honey buzzardsDates and longitudes on
 which oriental honey buzzards crossed 30, 25, 20, 15, 10, 5 and 0˚N during
 autumn and spring migration. Columns represent: bird ID, latitude bird
 crossed, season, and date and longitude on which bird crossed focal
 latitude.crossing_date_longitude.csvStopover data of oriental honey buzzardsDates and locations of stopovers by oriental honey buzzards. Columns represent: bird ID, year, date of arrival, date of departure, number of days bird spent in stopover site, and latitude and longitude of centroid of stopover site.stopovers.csvR scripts to estimate repeatabilities in oriental honey buzzards’ migrationThis file contains R scripts to estimate repeatabilities of dates and longitudes on which oriental honey buzzards crossed 30, 25, 20, 15, 10, 5 and 0˚N, and repeatabilities of arrival and departure dates, and latitudes and longitudes of centroids of, oriental honey buzzards’ stopovers.repeatability_estimate.R
DOI: 10.5061/dryad.73k278d
title: Data from: Is MHC diversity a better marker for conservation than neutral genetic diversity? a case study of two contrasting dolphin populations

description: Genetic diversity is essential for populations to adapt to changing
 environments. Measures of genetic diversity are often based on selectively
 neutral markers, such as microsatellites. Genetic diversity to guide
 conservation management, however, is better reflected by adaptive markers,
 including genes of the major histocompatibility complex (MHC). Our aim was
 to assess MHC and neutral genetic diversity in two contrasting bottlenose
 dolphin (Tursiops aduncus) populations in Western Australia—one apparently
 viable population with high reproductive output (Shark Bay) and one with
 lower reproductive output that was forecast to decline (Bunbury). We
 assessed genetic variation in the two populations by sequencing the MHC
 class II DQB, which encompasses the functionally important peptide binding
 regions (PBR). Neutral genetic diversity was assessed by genotyping
 twenty‐three microsatellite loci. We confirmed that MHC is an adaptive
 marker in both populations. Overall, the Shark Bay population exhibited
 greater MHC diversity than the Bunbury population—for example, it
 displayed greater MHC nucleotide diversity. In contrast, the difference in
 microsatellite diversity between the two populations was comparatively
 low. Our findings are consistent with the hypothesis that viable
 populations typically display greater genetic diversity than less viable
 populations. The results also suggest that MHC variation is more closely
 associated with population viability than neutral genetic variation.
 Although the inferences from our findings are limited, because we only
 compared two populations, our results add to a growing number of studies
 that highlight the usefulness of MHC as a potentially suitable genetic
 marker for animal conservation. The Shark Bay population, which carries
 greater adaptive genetic diversity than the Bunbury population, is thus
 likely more robust to natural or human‐induced changes to the coastal
 ecosystem it inhabits.
description: MHC sequence &
 micorsatellite diversity of bottlenose dolphinsThis supplementary data
 file contains the following: MHC class II DQB sequence alignment (Fig.
 A1); Microsatellite primer sequences and information on multiplexing and
 microsatellite alleles detected in dolphin populations (Table A1);
 Sampling information for conservative sampling approach (Table A2);
 Microsatellite and MHC II DQB diversity measures for East and West Shark
 Bay (Table A3); MHC II DQB sequence variants and BLASTN hits (GenBank)
 (Table A4); ANOVA test results, comparing microsatellite diversity
 measures between subsamples of the Shark Bay population (Table
 A5).Dryad
 supplementary data Manlik et al.
 2019.pdf