cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dm7cs86
title: Data from: Mating system variation in hybrid zones: facilitation, barriers and asymmetries to gene flow

description: Plant mating systems play a key role in structuring genetic variation both
 within and between species. In hybrid zones, the outcomes and dynamics of
 hybridization are usually interpreted as the balance between gene flow and
 selection against hybrids. Yet, mating systems can introduce selective
 forces that alter these expectations; with diverse outcomes for the level
 and direction of gene flow depending on variation in outcrossing and
 whether the mating systems of the species pair are the same or divergent.
 We present a survey of hybridization in 133 species pairs from 41 plant
 families and examine how patterns of hybridization vary with mating
 system. We examine if hybrid zone mode, level of gene flow, asymmetries in
 gene flow and the frequency of reproductive isolating barriers vary in
 relation to mating system/s of the species pair. We combine these results
 with a simulation model and examples from the literature to address two
 general themes: (i) the two-way interaction between introgression and the
 evolution of reproductive systems, and (ii) how mating system can
 facilitate or restrict interspecific gene flow. We conclude that examining
 mating system with hybridization provides unique opportunities to
 understand divergence and the processes underlying reproductive isolation.
description: HZmatingSystem_onlineDatabase of 133 plant hybrid zone studies and mating systems collected from the primary literature. See README.txt for additional information.
DOI: 10.5061/dryad.2c4n774
title: Data from: Nest attendance by tropical and temperate passerine birds: same constancy, different strategy

description: 1. Parental care in birds varies among species and geographic regions.
 Incubation behavior influences embryonic development rate and varies
 substantially among species. 2. We studied attendance at the nest by
 videoing nests or collecting data from the literature for 112 species in
 north temperate and lowland tropical sites, then associated patterns of
 incubation on- and off-bouts with species and environmental traits. 3.
 Songbirds nesting at low elevations incubate their eggs for an average of
 74.1% (12.9 s.d., n = 60 species) of the time in temperate regions and
 71.0% (12.2 s.d., n = 52 species) in tropical regions during daylight
 hours, and 84.3% (8.2 s.d.) and 85.3% (6.2 s.d.), respectively, of each
 24-hour cycle. 4. While these attendance percentages do not differ
 significantly between latitudes, our data also show that lowland tropical
 songbirds make fewer visits to the nest and, consequently, have longer
 on-bouts and off-bouts during incubation. This pattern in attendance
 reflects a latitudinal contrast in parental care strategy, where lowland
 tropical birds reduce visits to the nest by increasing on- and off-bout
 lengths while maintaining the same proportion of time spent incubating
 their eggs (constancy). 5. Similar constancy across latitude suggests that
 tropical and temperate birds may be similarly constrained to maintain
 elevated egg temperatures for normal embryo growth. 6. The different
 attendance strategies adopted in each region may reflect differences in
 ambient temperature, adult foraging time, and nest predation rate.
 Consistently warm ambient temperatures likely allow tropical birds to take
 longer off-bouts, and thereby to reduce activity around the nest, compared
 to temperate birds.
description: Austin_AttendanceAppendixIncubation attendance (diurnal constancy, total constancy, visit rate, on-bout length, off-bout length) and accompanying life-history or natural history traits from New World north temperate and lowland tropical passerines. Data sources are indicated in file.Austin_AdAttendanceAppendix_01302019.xlsx
DOI: 10.5061/dryad.nf5nk30
title: Data from: Genotype-specific effects of ericoid mycorrhizae on floral traits and reproduction in Vaccinium corymbosum

description: PREMISE OF THE STUDY: Most plants interact with mycorrhizal fungi and
 animal pollinators simultaneously. Yet, the effects of mycorrhizae on
 pollination are poorly understood. Here, we examined how inoculation with
 ericoid mycorrhizal fungi affected flowering phenology, floral traits, and
 reproductive success among eight genotypes of Vaccinium corymbosum
 (Ericaceae). We asked three overarching questions: 1) do genotypes differ
 in response to inoculation? 2) How does inoculation affect floral and
 flowering traits? 3) Are inoculated plants more attractive to pollinators
 and thus less pollen limited than non-inoculated plants of the same
 genotype? METHODS: To examine these questions, we experimentally
 inoculated plants with fungal spores at planting, grew them in the field,
 and took flowering and floral measurements over two years. In year two, we
 conducted a hand-pollination experiment to test if plants differed in
 pollen limitation. KEY RESULTS: Our results demonstrated that inoculated
 plants had significantly higher levels of colonization for some genotypes
 but not all, and there were significant floral trait changes in inoculated
 plants for some genotypes as well. On average, inoculated plants produced
 significantly larger floral displays, more fruits/inflorescence, and
 heavier fruits with lower sugar content, than non-inoculated, control
 plants. Hand pollination enhanced the production of fruits, and fruit
 mass, for non-inoculated plants but not for those that were inoculated.
 CONCLUSIONS: Our results demonstrate that ericoid mycorrhizal fungi
 enhance flowering and alter investment in reproduction in
 genotype-specific ways. These findings underscore the importance of
 examining belowground symbionts to fully understand the drivers of
 aboveground interactions.
description: Brody.et.al.2019.roots.dataProportion of blueberry root cortical cells occupied by ericoid mycorrhizal fungiBrody.et.al.2019.roots.csvBrody.et.al.2019.floral.displayCounts of blueberry inflorescence and flower number in plants with and without ericoid mycorrhizal fungus inoculationBrody.et.al.2019.floral.dimensionsMeasures of blueberry flower dimensions in plants with and without ericoid mycorrhizal fungus inoculationBrody.et.al.2019.pollen.limitationCounts of blueberry fruit production as a function of ericoid mycorrhizal fungus inoculation and pollen supplementation to flowersBrody.et.al.2019.pollen.limitation.berriesblueberry fruit mass, seed number, and sweetness (brix) as a function of ericoid mycorrhizal fungus inoculation and pollen supplementation to flowers
DOI: 10.5061/dryad.nc6d5f8
title: Data from: Diurnal variation around an optimum and near-critically high temperature does not alter the performance of an ectothermic aquatic grazer

description: The growing threat of global climate change has led to a profusion of
 studies examining the effects of warming on biota. Despite the potential
 importance of natural variability such as diurnal temperature
 fluctuations, most experimental studies on warming are conducted under
 stable temperatures. Here we investigated whether the responses of an
 aquatic invertebrate grazer (Lymnaea stagnalis) to an increased average
 temperature differ when the thermal regime is either constant or
 fluctuates diurnally. Using thermal-response curves for several
 life-history and immune defence traits, we first identified the optimum
 and near-critically high temperatures that Lymnaea potentially experience
 during summer heat waves. We then exposed individuals that originated from
 three different populations to these two temperatures under constant or
 fluctuating thermal conditions. After seven days, we assessed growth,
 reproduction, and two immune parameters (phenoloxidase-like activity and
 antibacterial activity of haemolymph) from each individual. Exposure to
 the near-critically high temperature led to increased growth rates and
 decreased antibacterial activity of haemolymph compared to the optimum
 temperature, whilst temperature fluctuations had no effect on these
 traits. The results indicate that the temperature level per se, rather
 than the variability in temperature was the main driver altering trait
 responses in our study species. Forecasting responses in
 temperature-related responses remains challenging, due to system-specific
 properties that can include intraspecific variation. However, our study
 indicates that experiments examining the effects of warming using constant
 temperatures can give similar predictions as studies with fluctuating
 thermal dynamics, and may thus be useful indicators of responses in
 nature.
description: Salo_et_al_Lymnaea_thermal_response_dataSalo_et_al_Lymnaea_responses_to_fluctuating_temperature
DOI: 10.5061/dryad.3m7875s
title: Data from: Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

description: The superb fairy-wren, Malurus cyaneus, is one of the most iconic
 Australian passerine species. This species belongs to an endemic
 Australasian clade, Meliphagides, which diversified early in the evolution
 of the oscine passerines. Today, the oscine passer- ines comprise almost
 half of all avian species diversity. Despite the rapid increase of
 available bird genome assemblies, this part of the avian tree has not yet
 been repre- sented by a high-quality reference. To rectify that, we
 present the first high-quality genome assembly of a Meliphagides
 representative: the superb fairy-wren. We com- bined Illumina shotgun and
 mate-pair sequences, PacBio long-reads, and a genetic linkage map from an
 intensively sampled pedigree of a wild population to gener- ate this
 genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was
 anchored onto 25 pseudochromosomes resulting in a final superscaffold N50
 of 68.11 Mb. This high-quality bird genome assembly is one of only a
 handful which is also accompanied by a genetic map and recombination
 landscape. In comparison to other pedigree-based bird genetic maps, we
 find that the fairy-wren genetic map more closely resembles those of
 Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis
 map which more closely resembles that of Gallus gallus. Lastly, we also
 provide a predictive gene and repeat annotation of the genome assembly.
 This new high-quality, annotated genome assembly will be an invaluable
 resource not only regarding the superb fairy-wren species and relatives
 but also broadly across the avian tree by providing a novel reference
 point for comparative genomic analyses.
description: Malurus cyaneus gene
 annotationGFF file containing the
 predictive gene annotation of the Malurus cyaneus
 genome.Malurus_cyaneus.final.withID.gffSliding window recombination rate (50Kb)Recombination rate in 50Kb nonoverlapping windows inferred from smoothing the Marey Map produced from LepMap3.RecombinationRates_LoessSmoothed_50kb.txtSliding window recombination rate (100Kb)Recombination rate in 100Kb nonoverlapping windows inferred from smoothing the Marey Map produced from LepMap3.RecombinationRates_LoessSmoothed_100kb.txtSliding window recombination rate (200Kb)Recombination rate in 200Kb nonoverlapping windows inferred from smoothing the Marey Map produced from LepMap3.RecombinationRates_LoessSmoothed_200kb.txtLM3 pedigree genotype inputInput for LepMap3 for which the genetic map was eventually inferred. Contains genotype likelihoods and family structure of the pedigree.2-LM3_ParentCall2.inputMalurus cyaneus genetic mapPedigree-based genetic map of Malurus cyaneus estimated using LM3. Includes all assembled whole chromosomes, sex averaged genetic distances, and sex-specific genetic distances.Malurus_cyaneus_geneticMap.txtMalurus cyaneus RepeatMasker OutputRepeat content information of the Malurus cyaneus genome.Malurus_cyaneus_RepeatMaskerOutput.tar.gz
DOI: 10.5061/dryad.2442n52
title: Data from: Holocene increases in palm abundances in northwestern Amazonia

description: Aim: In Amazonia, 227 of ca. 16,000 tree species account for half the
 individual trees (termed ‘hyperdominant’ species), and a disproportionate
 number of these species are palms. Our objectives are to show how and
 whether palm abundance has changed through the Holocene. Here, we
 reconstruct a detailed fire and vegetation history from northwestern
 Amazonia, with a focus on changes in palm abundances, and compare our
 results with regional data. Location: Amacayacu, Colombia Taxon: Amazonian
 palms Methods: We performed charcoal and phytolith analysis on soil cores,
 and obtained ages of past fires using 14C dating. We measured charcoal
 abundances and the relative abundances of phytoliths (silica-based
 microfossils) for all samples. We used these data to reconstruct changes
 in fire and vegetation, and compared these data with the species
 composition of palms in the modern forest. Results: Seven 14C dates from
 charcoal in three cores provided fire ages ranging from 1630 to 2450
 calibrated years before present. Charcoal was absent from one-third of the
 cores. Palm phytoliths from genera such as Iriartea, Socratea, and
 Astrocaryum have increased through time, while genera such as Euterpe,
 Hyospathe, and Oenocarpus have remained relatively stable and similar to
 modern levels. Overall, palm abundances were negatively correlated with
 charcoal measurements. Decorated sphere phytoliths, produced from unknown
 arboreal taxa were positively correlated with charcoal presence and
 abundance. Main conclusions: Palms have increased at Amacayacu and other
 forest plots through time, but the increases are largest in northwestern
 Amazonia. The presence of fire, however, dampens the increase in palms
 through time. When compared with reconstructions from other Amazon
 regions, our results suggest that increases in palm abundances in the late
 Holocene occurred both in the presence and absence of direct pre-Columbian
 human influence, and that response was strongest in northwestern Amazonia
 when human influence was minimal.
description: Holocene increases in
 palm abundances in northwestern Amazonia DATA FILEThis file contains the
 phytolith and charcoal data used in the publication "Holocene
 increases in palm abundances in northwestern Amazonia", by Heijink et
 al. The file also contains README sheet with all of the information for
 the various columns within the data sheet.Data_Manuscript_Amacayacu.xlsx
DOI: 10.5061/dryad.kn02d60
title: Data from: Pop‐off data storage tags reveal niche partitioning between native and non‐native predators in a novel ecosystem

description: 1. Niche partitioning might be predicted to be particularly dynamic in
 ‘novel ecosystems’ characterized by human-altered environmental conditions
 and biological invasions. Restoration efforts for native species in such
 systems can be informed by detailed characterization of niche
 partitioning. 2. In Lake Ontario, fishery management agencies have been
 engaged in a long-term struggle to restore native top predators including
 lake trout (Salvelinus namaycush). Meanwhile, management agencies continue
 to stock non-native species like Chinook salmon (Oncorhynchus tshawytscha)
 into the lake to support a recreational fishery and to help control the
 abundance of a non-native forage fish, the alewife (Alosa pseudoharengus).
 3. We used pop-off data storage tags to study fine scale (9.1M lines of
 data from 22 animals) behaviour and habitat use by lake trout (native) and
 Chinook salmon (non-native) in Lake Ontario in terms of depth and
 temperature, recorded at ≤70 s intervals for periods of up to 12 months.
 4. Chinook salmon occupied warmer and shallower waters during summer than
 did lake trout, and their niche breadth was wider. They achieved greater
 niche breadth in part because they were much more active vertically,
 cumulatively traveling 103±1 m hour-1 during summer (model-estimated
 median), whereas most lake trout were relatively inactive vertically (7±1
 m hour-1). In each of our analyses, there was more inter-individual
 variation among lake trout than among Chinook salmon, driven by some lake
 trout that spent considerable time making forays into warmer, shallower
 waters. 5. Synthesis and applications. Our results illustrate the
 different foraging tactics used by two species in the Great Lakes and
 reflect their distinct life histories. Vertical and thermal niche
 partitioning between Chinook salmon and lake trout helps to explain how
 these species can co-exist in a multi-species fishery even while having
 substantial overlap in diet. The diversity of behaviours exhibited here by
 native lake trout have likely helped them persist during dramatic changes
 to the forage base in recent decades; that flexibility could help underlie
 their long-term prospects for restoration during future changes to the
 ecosystem.
description: Raw data for Raby et al
 data storage tag paperDatafile is an .rds file
 - see README for instructions.dst_dataset_20190830.rds
DOI: 10.5061/dryad.h8b6vs2
title: Data from: Functional form and interactions of the drivers of understory non-native plant invasions in northern US forests

description: 1. The number and rate of non-native plant invasions in forests have been
 steadily increasing over the last century with profound consequences for
 the composition, structure and functioning of these ecosystems. While
 multiple regional, landscape and local environmental factors are known to
 drive the spread of non-native invasive plant species (NNIPS) into
 forests, such factors have rarely been analysed within a unified
 analytical framework allowing for the assessment of their relative
 importance, possible nonlinear behaviour, and interactions. Obtaining such
 knowledge would improve the understanding and allow prediction of forest
 plant invasions and help prioritize actions for effective NNIPS control
 and mitigation. 2. We used boosted regression trees and Bayesian nonlinear
 regression to analyse forest inventory data spanning 14 northern US states
 in combination with data on climate, land use and disturbance. Within each
 framework, we assessed the magnitude, direction and functional form of the
 effects of 18 regional to local environmental factors and their
 interactions on the probability of presence and richness of NNIPS in the
 forest understory, while controlling for sampling intensity, data
 collection time, and spatial autocorrelation. 3. The studied drivers
 together captured nearly 50% of the variation in NNIPS occurrence and
 richness and were sufficient to obtain sensible predictions. Most drivers
 exhibited monotonic nonlinear individual effects and several drivers
 showed non-additive combined effects. Temperature and landscape openness
 were the two major determinants of NNIPS presence and richness, but their
 effects were to a different degree moderated by elevation, climatic and
 topographic wetness, and stand age. Stand age was a more important
 predictor of NNIPS invasion than stand productivity. Deer density tended
 to be positively associated with NNIPS, while gypsy moth outbreaks
 possibly have increased resistance to plant invasions. 4. Synthesis and
 applications. To optimize non-native invasive plant species (NNIPS)
 control efforts in forests, it is important to explicitly account for the
 functional form and interactions among the factors operating across
 spatial and temporal scales. Increasing the average stand age at the
 landscape and regional levels is essential for buffering against further
 invasions. Recurrent canopy disturbance likely slowed down NNIPS invasion
 previously, yet whether this holds under higher propagule pressure remains
 unknown.
description: Golivets_JAPPL_2019_allDataThis file contains all the data used in the analyses, except for geographic coordinates of the study plots (in compliance with the FIA Program confidentiality requirements, those could not be released). All metadata are provided in Table 1 of the paper. Additionally, in the file, we provide an FIA plot identifier "PLT_CN", which can be used to match the selected plots to the FIA database.
DOI: 10.5061/dryad.nh08607
title: Data from: Early spring warming may hasten leaf emergence in Erythronium americanum

description: Premise of the study: Climate change is making spring arrive earlier than
 in the past, causing some species to alter the timing of their spring
 activities. This study addressed whether Erythronium americanum Ker Gawl.
 (trout lily), a common spring ephemeral, can hasten its spring emergence
 if exposed to early spring warming. Methods: I collected corms of E.
 americanum in the fall, overwintered them in soil, and exposed them to
 warming in either mid (early treatment) or late (late treatment) February.
 The timing of leaf emergence was monitored and compared between
 treatments. Key results: Leaves exposed to early warming emerged earlier
 than those in the late treatment. Bud break happened closer to date of
 exposure to warming in the late treatment than in the early treatment.
 Conclusions: Spring ephemerals may be able to produce leaves early in
 response to early spring warming induced by climate change. Risk of late
 frost and eventual shading by the canopy may limit the duration of a
 potentially extended growing season. Please be aware that if you ask to
 have your user record removed, we will retain your name in the records
 concerning manuscripts for which you were an author, reviewer, or editor.
 In compliance with data protection regulations, you may request that we
 remove your personal registration details at any time. (Use the following
 URL: https://www.editorialmanager.com/ajb/login.asp?a=r). Please contact
 the publication office if you have any questions.
description: EramBudBreakDataforDryadThese data show the Julian date of leaf emergence and days between exposure to warm temperatures and leaf emergence for Erythronium americanum plants exposed to early spring warming and more typical spring warming.
DOI: 10.5061/dryad.0k2s8k1
title: Data from: Dietary specialization is conditionally associated with increased ant predation risk in a temperate forest caterpillar community

description: The enemy-free space hypothesis (EFSH) contends that generalist predators
 select for dietary specialization in insect herbivores. At a community
 level, the EFSH predicts that dietary specialization reduces predation
 risk, and this pattern has been found in several studies addressing the
 impact of individual predator taxa or guilds. However, predation at a
 community level is also subject to combinatorial effects of multiple
 predator types, raising the question of how so-called multiple predator
 effects relate to dietary specialization in insect herbivores. Here we
 test the EFSH with a field experiment quantifying ant predation risk to
 insect herbivores (caterpillars) with and without the combined predation
 effects of birds. Assessing a community of 20 caterpillar species, we use
 model selection in a phylogenetic comparative framework to identify the
 caterpillar traits that best predict the risk of ant predation. A
 caterpillar species’ abundance, dietary specialization, and behavioral
 defenses were important predictors of its ant predation risk. Abundant
 caterpillar species had increased its risk of ant predation irrespective
 of bird predation. Caterpillar species with broad diet breadth and
 behavioral responsiveness to attack had reduced ant predation risk, but
 these ant effects only occurred when birds also had access to the
 caterpillar community. These findings suggest that ant predation of
 caterpillar species is density- or frequency-dependent, that ants and
 birds may impose countervailing selection on dietary specialization within
 the same herbivore community, and that contingent effects of multiple
 predators may generate behaviorally mediated life history trade-offs
 associated with herbivore diet breadth.
description: Singer et al E&E
 2019 data for DryadCalculation of effect
 sizes of ant and bird exclusion treatments on caterpillar
 densities.Character maps figure
 data v1Calculation of
 proportional effect size of ant exclusion on caterpillar density depicted
 in Figure 1.