cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mf287
title: Data from: Effect of craniofacial genotype on the relationship between morphology and feeding performance in cichlid fishes

description: The relationship between morphology and performance is complex, but
 important for understanding the adaptive nature of morphological
 variation. Recent studies have sought to better understand this system by
 illuminating the interconnectedness of different functional systems;
 however, the role of genetics is often overlooked. In this study, we
 attempt to gain insights into this relationship by examining the effect of
 genotypic variation at putative craniofacial loci on the relationship
 between morphology and feeding performance in cichlids. We studied two
 morphologically disparate species, as well as a morphologically
 intermediate hybrid population. We assessed feeding performance, jaw
 protrusion, and general facial morphology for each fish. We also genotyped
 hybrid animals at six previously identified craniofacial loci. Cichlid
 species were found to differ in facial geometry, kinematic morphology, and
 performance. Significant correlations were also noted between these
 variables; however, the explanatory power of facial geometry in predicting
 performance was relatively poor. Notably, when hybrids were grouped by
 genotype, the relationship between shape and performance improved. This
 relationship was especially robust in animals with the specialist allele
 at sox9b, a well-characterized regulator of craniofacial development.
 These data suggest a novel role for genotype in influencing complex
 relationships between form and function.
description: AllAnimalsDryadA list of all digitized videos with maximum raw prey velocity values from eachAllAnimalsMaxDryadA list of all the animals with morphological and genetic data. The prey velocity represents the highest value measured in any video of that animal. Prey velocity and protrusion are both listed before and after size correction.Analyze_DryadMatlab script that takes the x and y coordinates from each video and uses the linear distance between each consecutive frame to determine the velocity of the prey.Digitize_DryadMatlab script that consecutively opens each frame in the selected video, adjusts the contrast, and asks you to click on a point. It records the x and y coordinates of each selected point throughout the video.LandmarkRawXandY_DryadRaw X and Y coordinates of each landmark used in the PCA analyses. Points X12, Y12, X13, and Y13 are calibration points 1cm apart. This data was used for both PCA all and PCA hybrid.RScriptsDryadThis script was used for all correlations, models, and graphs as well as for the permutation analysis.
DOI: 10.5061/dryad.k018j
title: Data from: Evolution of invasive traits in nonindigenous species: increased survival and faster growth in invasive populations of rusty crayfish (Orconectes rusticus)

description: The importance of evolution in enhancing the invasiveness of species is
 not well understood, especially in animals. To evaluate evolution in
 crayfish invasions, we tested for differences in growth rate, survival,
 and response to predators between native and invaded range populations of
 rusty crayfish (Orconectes rusticus). We hypothesized that low conspecific
 densities during introductions into lakes would select for increased
 investment in growth and reproduction in invasive populations. We reared
 crayfish from both ranges in common garden experiments in lakes and
 mesocosms, the latter in which we also included treatments of predatory
 fish presence and food quality. In both lake and mesocosm experiments, O.
 rusticus from invasive populations had significantly faster growth rates
 and higher survival than individuals from the native range, especially in
 mesocosms where fish were present. There was no influence of within-range
 collection location on growth rate. Egg size was similar between ranges
 and did not affect crayfish growth. Our results, therefore, suggest that
 growth rate, which previous work has shown contributes to strong
 community-level impacts of this invasive species, has diverged since O.
 rusticus was introduced to the invaded range. This result highlights the
 need to consider evolutionary dynamics in invasive species mitigation
 strategies.
description: Crayfish growth and
 mortality dataThese are the data
 underlying the main crayfish growth mortality and findings in the
 manuscript
DOI: 10.5061/dryad.87js01tv
title: Data from: Polar lakes may act as ecological islands to aquatic protists

description: A fundamental question in ecology is whether microorganisms follow the
 same patterns as multicellular organisms when it comes to population
 structure and levels of genetic diversity. Enormous population sizes,
 predominately asexual reproduction, and presumably high dispersal due to
 small body size could have profound implications on their genetic
 diversity and population structure. Here, we have analyzed the population
 genetic structure in a lake-dwelling microbial eukaryote (dinoflagellate)
 and tested the hypothesis that there is population genetic differentiation
 among nearby lake subpopulations. This dinoflagellate occurs in the
 marine-derived saline lakes of the Vestfold Hills, Antarctica, which are
 ice-covered most of the year. Clonal strains were isolated from four
 different lakes, and were genotyped using AFLP (Amplified Fragment Length
 Polymorphism). Our results show high genetic differentiation among lake
 populations despite their close geographical proximity (&lt; 9 km).
 Moreover, genotype diversity was high within populations. Gene flow in
 this system is clearly limited, either due to physical or biological
 barriers. Our results discard the null hypothesis that there is free gene
 flow among protist lake populations. Instead, limnetic protist populations
 may differentiate genetically, and lakes act as ecological islands even on
 the microbial scale.
description: S_hangoei_AFLP_scoresDocumentation to S_hangoei_AFLP_scores This text file contains the scored AFLP data for Fst calculations and Structure runs. A total of 379 loci are included, 106 strains from four different populations. The first row (except column 1 and 2) contain the names of the loci (Loc_01 to Loc_379). The first column (as of row 2) contains the strain designation consisting of 4 letter and 2-3 numbers. SH represents species designation, i.e. Scrippsiella aft. hangoei (Dinophyceae), the next two letters indicate the lake from which the strain originates (AB=Abraxas, HI = Highway, MC = McNeil, VE = Vereteno; all lakes located in the Vestfold Hills, Antarctica), the last 2-3 digits represent the strain number. The third column (as of row 2) indicates lake population from which the strain originates. ABRA = Lake Abraxas, HIGH = Highway Lake, MCNEIL = McNeil Lake, VERE = Lake Vereteno. All subsequent columns give scores for presence of AFLP peaks. 1 = presence, 2 = absence of peak. There are no missing data.
DOI: 10.15468/dl.qf3n99
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hunzikeria texana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 116 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000922-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.725p9
title: Data from: Platelet GPIIb supports initial pulmonary retention but inhibits subsequent proliferation of melanoma cells during hematogenic metastasis

description: Platelets modulate the process of cancer metastasis. However, current
 knowledge on the direct interaction of platelets and tumor cells is mostly
 based on findings obtained in vitro. We addressed the role of the platelet
 fibrinogen receptor glycoprotein IIb (integrin αIIb) for experimental
 melanoma metastasis in vivo. Highly metastatic B16-D5 melanoma cells were
 injected intravenously into GPIIb-deficient (GPIIb-/-) or wildtype (WT)
 mice. Acute accumulation of tumor cells in the pulmonary vasculature was
 assessed in real-time by confocal videofluorescence microscopy. Arrest of
 tumor cells was dramatically reduced in GPIIb-/- mice as compared to WT.
 Importantly, we found that mainly multicellular aggregates accumulated in
 the pulmonary circulation of WT, instead B16-D5 aggregates were
 significantly smaller in GPIIb-/- mice. While pulmonary arrest of melanoma
 was clearly dependent on GPIIb in this early phase of metastasis, we also
 addressed tumor progression 10 days after injection. Inversely, and
 unexpectedly, we found that melanoma metastasis was now increased in
 GPIIb-/- mice. In contrast, GPIIb did not regulate local melanoma
 proliferation in a subcutaneous tumor model. Our data suggest that the
 platelet fibrinogen receptor has a differential role in the modulation of
 hematogenic melanoma metastasis. While platelets clearly support early
 steps in pulmonary metastasis via GPIIb-dependent formation of
 platelet-tumor-aggregates, at a later stage its absence is associated with
 an accelerated development of melanoma metastases.
description: Data
 _PONE-D-16-32451Data underlying main
 figures and supplement.
DOI: 10.5061/dryad.173r3j7
title: Data from: Mycorrhizal symbiosis increases the benefits of plant facilitative interactions

description: The diversity of pathways through which mycorrhizal fungi alter plant
 coexistence hinders the understanding of their effects on plant-plant
 interactions. The outcome of plant facilitative interactions can be
 indirectly affected by mycorrhizal symbiosis, ultimately shaping
 biodiversity patterns. We tested whether mycorrhizal symbiosis enhances
 plant facilitative interactions and whether its effect is consistent
 across different methodological approaches and biological scenarios. We
 conducted a meta-analysis of 215 cases (involving 21 nurse and 29
 facilitated species), in which the performance of a facilitated plant
 species is measured in the presence or absence of mycorrhizal fungi. We
 show that mycorrhizal fungi significantly enhance plant facilitative
 interactions mainly through an increment in plant biomass (aboveground)
 and nutrient content, although their effects differ across biological
 contexts. In semiarid environments mycorrhizal symbiosis enhances plant
 facilitation, while its effect is non-significant in temperate ecosystems.
 In addition, arbuscular but not ecto-mycorrhizal (EMF) fungi significantly
 enhances plant facilitation, particularly increasing the P content of the
 plants more than EMF. Some knowledge gaps regarding the importance of this
 phenomenon have been detected in this meta-analysis. The effect of
 mycorrhizal symbiosis on plant facilitation has rarely been assessed in
 other ecosystems different from semiarid and temperate forests, and rarely
 considering other fungal benefits provided to plants besides nutrients.
 Finally, we are still far from understanding the effects of the whole
 fungal community on plant-plant interactions, and on plant species
 coexistence.
description: Data set with all the
 references and variables used as factors in the
 meta-analyses.(1) Experimental
 conditions, (2) Mycorrhizal treatment, (3) Ecosystem, (4) Performance
 measurement, including plant part (4a) and type of nutrient (4b) and (5)
 Mycorrhizal type. The species of the nurse and the facilitated plants are
 presented with the mean, sample size (N) and standard error (SE) of the
 performance measurement reported for the facilitated plant. Data for the
 control and treated treatments are presented in different columns. We
 considered “treated” the treatment in which the mycorrhizal fungi were
 expected to be reduced. NA stands for not available
 data.Table
 S3_70.xls
DOI: 10.5061/dryad.p19v8
title: Data from: Sediment burial intolerance of marine macroinvertebrates

description: The marine environment contains suspended particulate matter which
 originates from natural and anthropogenic sources. Settlement of this
 material can leave benthic organisms susceptible to smothering, especially
 if burial is sudden i.e. following storms or activities such as dredging.
 Their survival will depend on their tolerance to, and their ability to
 escape from burial. Here we present data from a multi-factorial experiment
 measuring burial responses incorporating duration, sediment fraction and
 depth. Six macroinvertebrates commonly found in sediment rich environments
 were selected for their commercial and/or conservation importance.
 Assessments revealed that the brittle star (Ophiura ophiura), the queen
 scallop (Aequipecten opercularis) and the sea squirt (Ciona intestinalis)
 were all highly intolerant to burial whilst the green urchin (Psammichinus
 miliaris) and the anemone (Sagartiogeton lacerates), showed intermediate
 and low intolerance respectively, to burial. The least intolerant, with
 very high survival was the Ross worm (Sabellaria spinulosa). With the
 exception of C. intestinalis, increasing duration and depth of burial with
 finer sediment fractions resulted in increased mortality for all species
 assessed. For C. intestinalis depth of burial and sediment fraction were
 found to be inconsequential since there was complete mortality of all
 specimens buried for more than one day. When burial emergence was assessed
 O. ophiura emerged most frequently, followed by P. miliaris. The former
 emerged most frequently from the medium and fine sediments whereas P.
 miliaris emerged more frequently from coarse sediment. Both A. opercularis
 and S. laceratus showed similar emergence responses over time, with A.
 opercularis emerging more frequently under coarse sediments. The frequency
 of emergence of S. lacerates increased with progressively finer sediment
 and C. intestinalis did not emerge from burial irrespective of sediment
 fraction or depth. Finally, and perhaps unsurprisingly, the greatest
 ability to emerge from burial in all other species was from shallow (2 cm)
 burial. Although survival was consistently highly dependent on duration
 and depth of burial as expected, emergence behaviour was not as easily
 predictable thereby confounding predictions. We conclude that responses to
 burial are highly species specific and therefore tolerance generalisations
 are likely to be oversimplifications. These data may be used to inform
 environmental impact models that allow forecasting of the cumulative
 impacts of seabed disturbance and may provide mitigation measures for the
 sustainable use of the seabed.
description: Burial tolerance data
 for marine macroinvertebratesIndexed
 spreadsheetMultispecies
 Data.xlsx
DOI: 10.5061/dryad.rq6874m6
title: Data from: Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view

description: Asian wild rice (Oryza rufipogon) that ranges widely across the eastern
 and southern part of Asia is recognized as the direct ancestor of
 cultivated Asian rice (O. sativa). Studies of the geographic structure of
 O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a
 possible phylogeographic signal of subdivision in O. rufipogon. However,
 this signal of geographic differentiation is not consistently observed
 among different markers and studies, with often conflicting results. To
 more precisely characterize the phylogeography of O. rufipogon
 populations, a genome-wide survey of unlinked markers, intensively sampled
 from across the entire range of O. rufipogon is critical. In this study,
 we surveyed sequence variation at 42 genome-wide sequence tagged sites
 (STS) in 108 O. rufipogon accessions from throughout the native range of
 the species. Using Bayesian clustering, principal component analysis and
 amova, we conclude that there are two genetically distinct O. rufipogon
 groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation
 pattern generally from north-east to south-west. Different from many
 earlier studies, Ruf-I, which is found mainly in China and the Indochinese
 Peninsula, shows genetic similarity with one major cultivated rice
 variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the
 Indochinese Peninsula, is not found to be closely related to cultivated
 rice varieties. The other major cultivated rice variety, O. sativa
 japonica, is not found to be similar to either O. rufipogon groups. Our
 results support the hypothesis of a single origin of the domesticated O.
 sativa in China. The possible role of palaeoclimate, introgression and
 migration–drift balance in creating this clinal variation pattern is also
 discussed.
description: STS sequence alignments
 for O.rufipogonThere are 42 STS
 sequence alignments in FASTA format in the zip file. Each alignment
 include an outgroup sequence and 96 ingroup sequences (missing ones are
 not included). Name of each sequence start with a flow number and followed
 by sts number, organism/group annotation by IRRI, country of origin, IRGC
 number and chromosome number. Additional sample and loci information can
 be found in Table S1 and S2 of the supplementary information on Molecular
 Ecology website.sts_rufipogon.zip
DOI: 10.5061/dryad.fg86p
title: Data from: Widespread gene flow between oceans in a pelagic seabird species complex

description: Global-scale gene flow is an important concern in conservation biology as
 it has the potential to either increase or decrease genetic diversity in
 species and populations. Although many studies focus on the gene flow
 between different populations of a single species, the potential for gene
 flow and introgression between species is understudied, particularly in
 seabirds. The only well-studied example of a mixed-species, hybridizing
 population of petrels exists on Round Island, in the Indian Ocean.
 Previous research assumed that Round Island represents a point of
 secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific
 species (Pterodroma neglecta and Pterodroma heraldica). This study uses
 microsatellite genotyping and tracking data to address the possibility of
 between-species hybridization occurring outside the Indian Ocean.
 Dispersal and gene flow spanning three oceans were demonstrated between
 the species in this complex. Analysis of migration rates estimated using
 bayesass revealed unidirectional movement of petrels from the Atlantic and
 Pacific into the Indian Ocean. Conversely, structure analysis revealed
 gene flow between species of the Atlantic and Pacific oceans, with
 potential three-way hybrids occurring outside the Indian Ocean.
 Additionally, geolocation tracking of Round Island petrels revealed two
 individuals travelling to the Atlantic and Pacific. These results suggest
 that interspecific hybrids in Pterodroma petrels are more common than was
 previously assumed. This study is the first of its kind to investigate
 gene flow between populations of closely related Procellariiform species
 on a global scale, demonstrating the need for consideration of widespread
 migration and hybridization in the conservation of threatened seabirds.
description: Pterodroma
 microsatellite genotype datasetGenotypes for Pterodroma
 petrels generated in GeneMapper from final set of 12 autosomal
 microsatellite markers. Used in the manuscript for structure and gene flow
 analysis.Genotype dataset for
 analysis.csv
DOI: 10.5061/dryad.457f7
title: Data from: The evolution of photosynthetic anatomy in Viburnum (Adoxaceae)

description: Premise of research: Leaf mesophyll is often differentiated into a
 palisade layer with tightly packed, elongated cells (I-cells) and a spongy
 layer with loosely packed, complex shaped cells. An alternative palisade
 type, composed of branched H-cells, has evolved in a number of plant
 lineages. Viburnum (Adoxaceae) possesses both types of palisade, providing
 an opportunity to assess the significance of evolutionary switches between
 these forms. Methodology: An anatomical survey of 80 species spanning the
 Viburnum phylogeny permitted an analysis of palisade differences in
 relation to other characters. A geometric model of leaf mesophyll surface
 area for CO2 absorption correlated well with measured photosynthetic
 capacity in a subset of species, allowing us to infer shifts in
 photosynthetic function. Pivotal results: Ancestrally, viburnums probably
 produced a palisade with one layer of H-cells. Multiple transitions to two
 layers of H-cells (H2) and to one or two layers of I-cells (I1, I2)
 occurred. These shifts were correlated with increases in photosynthetic
 capacity, and H2 appear functionally equivalent to I1 with respect to CO2
 absorption. Conclusions: Photosynthetic anatomy H2 and I1 palisade may
 represent alternative evolutionary solutions for increasing leaf CO2
 absorption. Additionally, H-cells and I-cells might perform differently
 with respect to light absorption and/or drought tolerance. The evolution
 of I-palisade cells may thus have tracked movements into open
 environments, while H2 could increase photosynthetic capacity in the
 forest understory.
description: PhylogenyBayesian 50% majority rule consensus tree.datasetHabitat, leafing habit and anatomical data used for the comparative analysis.
DOI: 10.6084/m9.figshare.31153353
title: Data and Repository from Evidence of Bird-Like Foot Function in Tyrannosaurus

description: The complete data set including specimen data, as well as the variables used with each formula with each foot-strike pattern, hip height, and RSL. This file also includes a guide, and further information on potential top speeds that were best supported based on the authorsâ€™ readings of previous literature at the time of writing, and images used in the main manuscript.
DOI: 10.6084/m9.figshare.31153353.v1
title: Data and Repository from Evidence of Bird-Like Foot Function in Tyrannosaurus

description: The complete data set including specimen data, as well as the variables used with each formula with each foot-strike pattern, hip height, and RSL. This file also includes a guide, and further information on potential top speeds that were best supported based on the authorsâ€™ readings of previous literature at the time of writing, and images used in the main manuscript.