cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0p928qb
title: Data from: Assessing behavioral associations in a hybrid zone through social network analysis: complex assortative behaviors structure associations in a hybrid quail population

description: Behavior can strongly influence rates and patterns of hybridization
 between animal populations and species. Yet, few studies have examined
 reproductive behaviors in natural hybrid zones within the fine-scale
 social structure in which they take place. We use radio-frequency
 identification (RFID) tags with social network analyses to test whether
 phenotypic similarity in plumage and mass correlate with social behavior
 throughout a breeding season in a California and Gambel’s quail hybrid
 zone. We use a novel approach to partition phenotypic variation in a way
 that does not confound differences between sexes and species, and
 illustrate the complex ways that phenotype and behavior structure the
 social environment, mating opportunities, and male-male associations.
 Associations within the admixed population were random with respect to
 species-specific plumage, but showed strong patterns of assortment based
 upon sexually dimorphic plumage, monomorphic plumage, and mass. Weak
 behavioral reproductive isolation in this admixed population may be the
 result of complex patterns of phenotypic assortment based upon multiple
 traits, rather than a lack of phenotypic discrimination. More generally,
 our results inform the utility of social network analyses for analyzing
 behavioral factors affecting genetic exchange between populations and
 species.
description: Raw RFID
 ReadsRaw reads of RFID-tagged
 quail from the Royal Carrizo population during the 2016 breeding season.
 Quail were detected at 16 RFID reader-equipped feeding stations positioned
 in brushy areas with high quail activity within the
 population.rawReads.csvRaw Phenotype DataRaw phenotype data of quail from across the hybrid zone. Plumage color trait values were calculated with the MicaToolbox plugin in ImageJ, and are presented with separate measures for Hue, Saturation, and Value. The trait "proportion_scaling" is a measure of the scaling pattern on the vent of birds (present in C. californica and absent in C. gambelii) and was measured as the proportion of black pixels within a standard ROI on the breast after thresholding images in ImageJ to pure black and white values (see manuscript Appendix for details). Mass, plume length, and throat length are morphometric values that were measured in the field.rawTraits.csv
DOI: 10.5061/dryad.hg19c6n
title: Data from: Forest succession and climate variability interacted to control fire activity over the last four centuries in an Alaskan boreal landscape

description: Context: The boreal forest is globally important for its influence on
 Earth’s energy balance, and its sensitivity to climate change. Ecosystem
 functioning in boreal forests is shaped by fire activity, so anticipating
 the impacts of climate change requires understanding the precedence for,
 and consequences of, climatically induced changes in fire regimes.
 Long-term records of climate, fire, and vegetation are critical for
 gaining this understanding. Objectives: We investigated the relative
 importance of climate and landscape flammability as drivers of fire
 activity in boreal forests by developing high-resolution records of fire
 history, and characterizing their centennial-scale relationships to
 temperature and vegetation dynamics. Methods: We reconstructed the timing
 of fire activity in interior Alaska, USA, using seven lake-sediment
 charcoal records spanning CE 1550–2015. We developed individual and
 composite records of fire activity, and used correlations and qualitative
 comparisons to assess relationships with existing records of vegetation
 and climate. Results: Our records document a dynamic relationship between
 climate and fire. Fire activity and temperature showed stronger coupling
 after ca. 1900 than in the preceding 350 yr. Biomass burning and
 temperatures increased concurrently during the second half of the
 twentieth century, to their highest point in the record. Fire activity
 followed pulses in black spruce establishment. Conclusions: Fire activity
 was facilitated by warm temperatures and landscape-scale dominance of
 highly flammable mature black spruce, with a notable increase in
 temperature and fire activity during the twenty-first century. The results
 suggest that widespread burning at landscape scales is controlled by a
 combination of climate and vegetation dynamics that together drive
 flammability.
description: Hoecker_and_Higuera_2019_LandscapeEcologyThis repository contains data and code associated with: Hoecker TJ, Higuera PE. 2019. Forest succession and climate variability interacted to control fire activity over the last four centuries in an Alaskan boreal forest. *Landscape Ecology* DOI: doi.org/10.1007/s10980-018-00766-8
DOI: 10.7927/v4mp-d627
title: IPCC AR6 Synthesis Report LR Figure 2.5 (b): Projected emission outcomes from near-term policy assessments for 2030

description: This panel shows a snapshot of the GHG emission ranges of the four modelled pathways in 2030: the trend from implemented policies, the limit to 2°C (&gt;67%) or return warming to 1.5°C (&gt;50%) after a high overshoot NDC's until 2030, the limit warning to 2°C (&gt;67%) with immediate action and the limit to 1.5°C (&gt;50%) with no or limited overshoot. This panel displays the projected emissions outcomes from near-term policy assessments in 2030. GHG emissions are in CO2-equivalent using GWP100 from AR6 WG I.
DOI: 10.15468/dl.7e36yr
title: Occurrence Download

description: A dataset containing 43477 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is Ambrosia artemisiifolia"
 ]
}

 The dataset includes 43477 records from 267 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001563-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q0f84nh
title: Data from: Were bivalves ecologically dominant over brachiopods in the late Paleozoic? A test using exceptionally preserved fossil assemblages

description: Interpreting changes in ecosystem structure from the fossil record can be
 challenging. In a prominent example, the traditional view that brachiopods
 were ecologically dominant over bivalves in the Paleozoic has been
 disputed on both taphonomic and metabolic grounds. Aragonitic bivalves may
 be underrepresented in many fossil assemblages due to preferential
 dissolution. Abundance counts may further understate the ecological
 importance of bivalves because they tend to have more biomass and higher
 metabolic rates than brachiopods. We evaluate the relative importance of
 the two clades in exceptionally preserved, bulk-sampled fossil assemblages
 from the Pennsylvanian Breathitt Formation of Kentucky, where aragonitic
 bivalves are preserved as shells, not molds. At the regional scale,
 brachiopods were twice as abundant as bivalves and were collectively
 equivalent in biomass and energy use. Analyses of samples from the
 Paleobiology Database that contain abundance counts are consistent with
 these results and show no clear trend in the relative ecological
 importance of bivalves during the middle and late Paleozoic. Bivalves were
 probably more important in Paleozoic ecosystems than is apparent in many
 fossil assemblages, but they were not clearly dominant over brachiopods
 until after the Permian-Triassic extinction, which caused the shelly
 benthos to shift from bivalve and brachiopod dominated to merely bivalve
 dominated.
description: Breathitt Formation
 Supplementary TablesIncludes the fossil
 assemblage localities, species abundance information, individual size
 measurements, and average size and metabolic estimates for bivalves and
 brachiopodsSupplementary
 Tables.docxSupplementary File 1 --
 Bivalves Phanerozoic refsPBDB Data used for
 bivalves in the fig. 1 diversity curveBivalves Phanerozoic
 refs.csvSupplementary file 2 --
 Brachs Phanerozoic refsPBDB Data used for
 brachiopods in the fig. 1 diversity curve.Brachs Phanerozoic
 refs.csvGlobal analysis
 supplement part 1PBDB Data (Ordovician -
 Permian) used for global analysis in fig. 9.Brach-Biv-Ord-Perm-pbdb_data-refs.csvGlobal analysis supplement part 2PBDB Data (Triassic-Jurassic) used for global analysis in fig. 9.Brach-Biv-Tr-Jur-pbdb_data_refs.csv
DOI: 10.5061/dryad.b2c58pc
title: Data from: Origin and evolution of the octoploid strawberry genome

description: Cultivated strawberry emerged from the hybridization of two wild octoploid
 species, both descendants from the merger of four diploid progenitor
 species into a single nucleus more than 1 million years ago. Here we
 report a near-complete chromosome-scale assembly for cultivated octoploid
 strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary
 processes that shaped this complex allopolyploid. We identified the extant
 relatives of each diploid progenitor species and provide support for the
 North American origin of octoploid strawberry. We examined the dynamics
 among the four subgenomes in octoploid strawberry and uncovered the
 presence of a single dominant subgenome with significantly greater gene
 content, gene expression abundance, and biased exchanges between
 homoeologous chromosomes, as compared with the other subgenomes. Pathway
 analysis showed that certain metabolomic and disease-resistance traits are
 largely controlled by the dominant subgenome. These findings and the
 reference genome should serve as a powerful platform for future
 evolutionary studies and enable molecular breeding in strawberry.
description: Cam_Genome_Dryad_2019Genome assembly and annotation files; intermediate and output files from PhyDs phylogenetic analyses
DOI: 10.5061/dryad.1723h44
title: Data from: Seed predation increases from the Arctic to the Equator and from high to low elevations

description: Species interactions have long been predicted to increase in intensity
 toward the tropics and low elevations because of gradients in climate,
 productivity, or biodiversity. Despite their importance for understanding
 global ecological and evolutionary processes, plant-animal interaction
 gradients are particularly difficult to test systematically across large
 geographic gradients, and evidence from smaller, disparate studies is
 inconclusive. By systematically measuring postdispersal seed predation
 using 6995 standardized seed depots along 18 mountains in the Pacific
 cordillera, we found that seed predation increases by 17% from the Arctic
 to the Equator and by 17% from 4000 meters above sea level to sea level.
 Clines in total predation, likely driven by invertebrates, were consistent
 across treeline ecotones and within continuous forest and were better
 explained by climate seasonality than by productivity, biodiversity, or
 latitude. These results suggest that species interactions play predictably
 greater ecological and evolutionary roles in tropical, lowland, and other
 less seasonal ecosystems.
description: Hargreaves2019SciAdv_data1 seedpredation perseedtypeXcagetreatXsiteXdateSeed predation data used for analyses in Fig. 1 and Table 1. Seed predation data are averaged across 10 to 20 depots per seed type (sunflower or oat) per site per date.Hargreaves2019SciAdv_data2 seedpredation perseedtypeXcagetreatXsite & covariatesMean seed predation intensity per site (for each seed type) and environmental covariates (climate, productivity, vertebrate richness) tested in structural equation models.
DOI: 10.5061/dryad.1m04tv1
title: Data from: On the importance of habitat continuity for delimiting biogeographic regions and shaping richness gradients

description: The formation and maintenance of biogeographic regions and the latitudinal
 gradient of species richness are thought to be influenced, in part, by the
 spatial distribution of physical habitat (habitat continuity). But the
 importance of habitat continuity in relation to other variables for
 shaping richness gradients and delimiting biogeographic regions has not
 been well established. Here, we show that habitat continuity is a top
 predictor of biogeographic structure and the richness gradient of eastern
 Pacific rocky shore gastropods (spanning ~23,000 km, from 43ºS-48ºN).
 Rocky shore habitat continuity is generally low within
 tropical/subtropical regions (compared to extratropical regions), but
 particularly at biogeographic boundaries where steep richness gradients
 occur. Regions of high rocky shore habitat continuity are located towards
 the centres of biogeographic regions where species turnover tends to be
 relatively low. Our study highlights the importance of habitat continuity
 to help explain patterns and processes shaping the biogeographic
 organization of species.
description: Fenberg&Rivadeneira_ELE_DataData for the (1) the distribution and size of each habitat gap along the transect; (2), the % of rocky shore within each bin, categorised by the centre and edge sections of each biogeographic region and across all regions, and by whether a bin is tropical/extratropical; (3) Environmental data for the random forest analyses, including habitat continuity; (4) the species presence/absence matrix; (5) range extent data for each species totally within the transect; (6) species richness across the transect.
DOI: 10.5061/dryad.k388cn8
title: Data from: Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species

description: Palaeoclimatic events and biogeographical processes since the mid-Tertiary
 have played an important role in shaping the evolution and distribution of
 Australian fauna. However, their impacts on fauna in southern and arid
 zone regions of Australia are not well understood. Here we investigate the
 phylogeography of an Australian scincid lizard, Tiliqua rugosa, across
 southern Australia using mitochondrial DNA (mtDNA) and 11 nuclear DNA
 markers (nuDNA), including nine anonymous nuclear loci. Phylogenetic
 analyses revealed three major mtDNA lineages within T. rugosa,
 geographically localised north and south of the Murray River in southern
 Australia, and west of the Nullarbor Plain. Molecular variance and
 population analyses of both mtDNA and nuDNA haplotypes revealed
 significant variation among the three populations, although potential
 introgression of nuDNA markers was also detected for the Northern and
 Southern population. Coalescent times for major mtDNA lineages coincide
 with an aridification phase, which commenced after the early Pliocene and
 increased in intensity during the Late Pliocene-Pleistocene. Species
 distribution modelling and a phylogeographic diffusion model suggest that
 the range of T. rugosa may have contracted during the Last Glacial Maximum
 and the locations of optimal habitat appear to coincide with the
 geographic origin of several distinct mtDNA lineages. Overall, our
 analyses suggest that Plio-Pleistocene climatic changes and biogeographic
 barriers associated with the Nullarbor Plain and Murray River have played
 a key role in shaping the present-day distribution of genetic diversity in
 T. rugosa and many additional ground-dwelling animals distributed across
 southern Australia.
description: Dryad data for Ansari et
 al. MPE 2019Population data from ANM
 nuclear lociDryad.zip
DOI: 10.5061/dryad.4053d31
title: Data from: The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

description: Background: Repetitive sequences, including transposable elements (TEs)
 and satellite DNAs, occupy a considerable portion of plant genomes.
 Analysis of the repeat fraction benefits the understanding of genome
 structure and evolution. Spinach (Spinacia oleracea L.), an important
 vegetable crop, is also a model dioecious plant species for studying sex
 determination and sex chromosome evolution. However, the repetitive
 sequences of the spinach genome have not been fully investigated. Results:
 We extensively analyzed the repetitive components of draft spinach genome,
 especially TEs and satellites, by different strategies. A total of 16,002
 full-length TEs were identified. Among the most abundant long terminal
 repeat (LTR) retrotransposons (REs), Copia elements were overrepresented
 compared with Gypsy ones. Angela was the most dominating Copia lineage;
 Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of
 LTR-REs was 1.42 million years; approximately 83.7% of these elements were
 retrotransposed during the last two million years. RepeatMasker totally
 masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and
 DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence
 in situ hybridization (FISH) analysis showed that most LTR-REs dispersed
 all over the chromosomes, by contrast, elements of CRM lineage were
 distributed at the centromeric region of all chromosomes. In addition,
 Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites
 Spsat2 and Spsat3 were exclusively located at the telomeric region of the
 short arm of sex chromosomes. Conclusions: We reliably annotated the TE
 fraction of the draft genome of spinach. FISH analysis indicates that
 Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might
 participate in sex chromosome formation and evolution. Based on FISH
 signals of microsatellites, together with 45S rDNA, a fine karyotype of
 spinach was established. This study improves our knowledge of repetitive
 sequence organization in spinach genome and aids in accurate spinach
 karyotype construction.
description: Full length TE seqeunces
 of spinachThese data were analyzed
 as a part of the following publicaiton: " The landscape of
 transposable elements and satellite DNAs in the genome of a dioecious
 plant spinach (Spinacia oleracea L.)" A separate fasta file is
 available in Dryad. Each sequence in the file represents a full-length TE
 analyis using the methods described in the paper. The header for each
 sequence includes a title followed by the annotation for that particular
 element.spinach_full_length_TE.fastaConsensus TE sequences analyzed by RepeatExplorer in spinach genomespinach_repeatmodeler.fasta
DOI: 10.5061/dryad.vc7cf5m
title: Data from: Different roles of elevational and local environmental factors on abundance-based beta diversity of the soil Enchytraeidae on the Changbai Mountain

description: The elevational alpha biodiversity gradient in mountain regions is one of
 the well-known ecological patterns, but its beta diversity pattern remains
 poorly-known. Examining the beta diversity and its components could
 enhance the understanding of community assembly mechanism. We studied the
 beta diversity pattern of the soil enchytraeids along a distinct
 elevational gradient (705—2280 m) on the Changbai Mountain, the
 best-preserved mountain in northeastern China. The overall abundance-based
 community dissimilarity was relatively high (ca. 0.70), largely due to the
 balanced-variation component (85%). The overall dissimilarity and its
 balanced-variation (substitution) component were both related to local
 environmental heterogeneity and elevational distance, with the
 environmental relationships being stronger. In contrast, the
 abundance-gradient (subsets) component was not related to the two
 gradients. The same important spatial and environmental variables were
 detected in structuring overall dissimilarity and substitution component,
 different from that in subsets component. Variation partitioning analysis
 showed that environmental control played a more important role than
 spatial (vertical and horizontal) factors in structuring the patterns of
 overall beta diversity and its two components. The predictive power of
 multivariate analysis was higher for the substitution component (nearly
 50%) and overall dissimilarity (35%), but much lower for subsets
 components (&lt; 4%). These findings implied that abundance-based beta
 diversity patterns of the soil enchytraeids were the results of different
 ecological processes (e.g. environmental sorting and dispersal
 limitation), operating in the two antithetic components. Our study showed
 the substitution and loss of individuals reflecting different ecological
 processes and highlights the importance of partitioning beta diversity in
 assessing biodiversity patterns and their causes.
description: enchytraeid
 assemblages
DOI: 10.5061/dryad.60j73s7
title: Data from: Infection sequence alters disease severity—Effects of the sequential exposure of two larval trematodes to Polypedates cruciger tadpoles

description: Multiple pathogens co-exist in nature and the sequence in which the host
 encounters the parasites influences interactions between parasites and
 host pathology. Here the effects of infection by two larval trematodes,
 pleurolophocercous cercariae of Acanthostomum burminis and a furcocercous
 cercariae, on common hourglass tree frog (Polypedates cruciger) was
 examined. Ten days post-hatch tadpoles (Gosner stage 27/28) were used for
 infection exposures. First, infection of individuals was carried out by
 introducing each cercariae type to the tadpoles separately. Second,
 co-infection of the two cercariae was carried out by alternating the
 sequences of exposure. For all the experiments, appropriate controls were
 instituted. Tadpoles exposed to parasites had lower survival compared to
 controls. The highest survival was observed in the co-infection when
 furcocercous was introduced first (82.5%). The lowest survival was
 observed in the co-infection when the A. burminis cercariae was introduced
 first (65.0%). In co-infections, when A. burminis was introduced prior to
 furcocercous, survival of the tadpoles was reduced by 17.0% compared to
 the exposures of furcocercous prior to A. burminis. Prior infection with
 A. burminis induced negative effect on the host with an increased
 infection severity while prior infection with furcocercous had reduced
 infection severity than lone exposures. These results suggest that
 furcocercous infections can be beneficial for hosts challenged with A.
 burminis provided that A. burminis exposure occurs second. None of the
 treatments had an effect on the growth of the tadpoles but lengthening of
 developmental period was observed in some exposures. All exposed tadpoles
 developed malformations which were exclusively axial – kyphosis and
 scoliosis. However, there was no difference in the number of malformed
 individuals in the single infection (19.0-25.0%) compared to co-infection
 (20.0-22.5%) or between coinfections. The results suggest that the
 sequence of parasite exposure affects host parasite interactions and hence
 the disease outcomes.
description: cysts numbers in 4
 treatmentsMean number of cysts
 disappearance in 4 treatmentscysts
 numbers.csvgrowth of the survived
 tadpolesThe file consists the
 growth measurements of the survived tadpoles as length, weight and time to
 metamorph (TE50)growth.csv