cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d7p3b40
title: Data from: Annual ring growth of a widespread high-arctic shrub reflects past fluctuations in community-level plant biomass

description: 1. Long time-series of primary production are rarely available,
 restricting our mechanistic understanding of vegetation and ecosystem
 dynamics under climate change. Dendrochronological tools are increasingly
 used instead, particularly in the Arctic – the world’s most rapidly
 warming biome. Yet, high-latitude plant species are subject to strong
 energy allocation trade-offs, and whether annual allocations to secondary
 growth (e.g. ‘tree-rings’) actually reflects primary production
 above-ground remains unknown. Taking advantage of a unique ground-based
 monitoring time-series of annual vascular plant biomass in high Arctic
 Svalbard (78N), we evaluated how well retrospective ring growth of the
 widespread dwarf shrub Salix polaris represents above-ground biomass
 production of vascular plants. 2. Using a balanced design in permanent
 plots for plant biomass monitoring, we collected 30 S. polaris shrubs
 across five sites in each of two habitats. We established annual ring
 growth time-series using linear mixed-effects models and related them to
 local weather records and 13 years of above-ground biomass production in
 six habitats. 3. Annual ring growth was positively correlated with
 above-ground biomass production of both S. polaris (r = 0.56) and the
 vascular plant community as a whole (r = 0.70). As for above-ground
 biomass, summer temperature was the main driver of ring growth, with this
 ecological signal becoming particularly clear when accounting for plant,
 site and habitat heterogeneity. The results suggest that ring growth
 measurements performed on this dominating shrub can be used to track
 fluctuations in past vascular plant production of high-arctic tundra. 4.
 Synthesis. Dendrochronological tools are increasingly used on arctic
 shrubs to enhance our understanding of vegetation dynamics in the world’s
 most rapidly warming biome. Fundamental to such applications is the
 assumption that annual ring growth reflects between-year variation in
 above-ground biomass production. Here we showed that ring growth indeed
 was a robust proxy for the annual above-ground productivity of both the
 focal shrub and the vascular plant community as a whole. Despite the
 challenges of constructing ring growth chronologies from irregularly
 growing arctic shrubs, our findings confirm that shrub dendrochronology
 can open new opportunities for community-dynamic studies under climate
 change, including in remote places where annual field sampling is
 difficult to achieve.
description: rwl_SemmeldalenCross-section raw ring-widths (micrometers) in format "Tucson". See the associated file "Shrub_Semmeldalen_info".Shrub_Semmeldalen_infoDescription of the individual cross-sections with a description of the column names in the second sheet of this document.Semmeldalen LME outputRing growth and above-ground biomass time-series obtained from linear mixed-effects models. See the description of the column names in the second sheet of this document.
DOI: 10.5061/dryad.n13h839
title: Data from: Genetically determined fungal pathogen tolerance and soil variation influences ectomycorrhizal traits of loblolly pine

description: 1. Selection on genetically correlated traits within species can create
 indirect effects on one trait by selection on another. The consequences of
 these trait correlations are of interest because they may influence how
 suites of traits within species evolve under differing selection
 pressures, both natural and artificial. 2. By utilizing genetic families
 of loblolly pine either tolerant (t) or susceptible (s) to two different
 suites of pathogenic fungi responsible for causing either pine decline
 (PD) or fusiform rust (FR) disease, we investigated trait variation and
 trait correlations within loblolly pine (Pinus taeda L.) by determining
 how ectomycorrhizal (EM) colonization relates to pathogen susceptibility.
 3. We detected interactions between susceptibility to pathogenic fungi and
 soil inoculation source on loblolly pine compatibility with the EM fungi
 Thelephora, and on relative growth rate of loblolly pine. Additionally, we
 detected spatial variation in the loblolly pine – EM fungi interaction,
 and found that variation in colonization rates by some members of the EM
 community is not dictated by genetic variation in the host plant but
 rather soil inoculation source alone. 4. The work presented here
 illustrates the potential for indirect selection on compatibility with
 symbiotic EM fungi as a result of selection for resistance to fungal
 pathogens. Additionally, we present evidence that the host plant does not
 have a single ‘mycorrhizal trait’ governing interactions with all EM
 fungi, but rather that it can interact with different fungal taxa
 independently. 5. Synthesis. An understanding of the genetic architecture
 of essential traits in focal species is crucial if we are to anticipate
 and manage the results of natural and artificial selection. As
 demonstrated here, an essential but often overlooked symbiosis (that
 between plants and mycorrhizal fungi) may be indirectly influenced by
 directed selection on the host plant.
description: Piculell etal EM
 colonization dataPiculelletal_EMcolonizationdata.csv
DOI: 10.5061/dryad.5jh27
title: Data from: Two genomic regions together cause dark abdominal pigmentation in Drosophila tenebrosa

description: Pigmentation is a rapidly evolving trait that is under both natural and
 sexual selection in many organisms. In the quinaria group of Drosophila,
 nearly all of the 30 species have an abdomen that is light in color with
 distinct markings; D. tenebrosa is the exception in that it has a
 completely melanic abdomen with no visible markings. In this study, we use
 a combination of quantitative genetic and candidate gene approaches to
 investigate the genetic basis of abdominal pigmentation in D. tenebrosa.
 We find that abdominal pigmentation is invariant across wild- caught lines
 of D. tenebrosa and is not sexually dimorphic. Quantitative genetic
 mapping utilizing crosses between D. tenebrosa and the light-colored D.
 suboccidentalis indicates that two genomic regions together underlie
 abdominal pigmentation, including the X-chromosome and an autosome (Muller
 Element C/E). Further support for their central importance in pigmentation
 is that experimental introgression of one phenotype into the other
 species, in either direction, results in introgression of these two
 genomic regions. Finally, the expression of the X- linked gene yellow in
 the pupae exactly foreshadows the adult melanization pattern in the
 abdomen of both species, suggesting that changes in the regulation of
 yellow are important for the phenotypic divergence of D. tenebrosa from
 the rest of the quinaria group. These results contribute to a body of work
 that demonstrates how changes in expression of highly conserved genes can
 cause substantial phenotypic differences even between closely related
 species.
description: BC_dataGenotype and phenotype data from backcrosses.introgression genotypesGenotypes and phenotypes of males from introgressionsintrogression data.txt
DOI: 10.5061/dryad.4gt21
title: Data from: Spatial patterns and predictors of trophic control in marine ecosystems

description: A key question in ecology is under which conditions ecosystem structure
 tends to be controlled by resource availability vs. consumer pressure.
 Several hypotheses derived from theory, experiments and observational
 field studies have been advanced, yet a unified explanation remains
 elusive. Here, we identify common predictors of trophic control in a
 synthetic analysis of 52 observational field studies conducted within
 marine ecosystems across the Northern Hemisphere and published between
 1951 and 2014. Spatial regression analysis of 45 candidate variables
 revealed temperature to be the dominant predictor, with unimodal effects
 on trophic control operating both directly (r2 = 0.32; P &lt; 0.0001)
 and indirectly through influences on turnover rate and quality of primary
 production, biodiversity and omnivory. These findings indicate that
 temperature is an overarching determinant of the trophic dynamics of
 marine ecosystems, and that variation in ocean temperature will affect the
 trophic structure of marine ecosystems through both direct and indirect
 mechanisms.
description: Interactions between
 time-series of marine predators and preyData file contains
 correlations between time-series of marine predators and their prey, as
 reported in the scientific literature, as well as average biophysical
 variables at the location where the correlations were derived. The
 associated README file contains descriptions of all
 variables.Boyce_etal_2015_ELE_database.csv
DOI: 10.5061/dryad.q1m54
title: Data from: Context-dependent alarm signalling in an insect

description: Animals often respond to danger by raising alarm to inform others. Alarm
 signals come in many different forms, such as visual or mechanical
 display, sound or odour. Some animals produce vocal alarm signals that
 vary with the level of danger. For chemical alarm signals, virtually
 nothing is known about such context-dependent signalling due to a general
 notion that alarm pheromones have fixed compositions. Here, we show that
 larvae of the Western Flower Thrips (Frankliniella occidentalis) produce
 an alarm pheromone whose composition varies with the level of danger they
 face: the presence of a relatively harmless predator or a very dangerous
 predator, that is either actually attacking or not. The frequency of alarm
 pheromone excretion increases with the level of danger. Moreover, the
 composition of excreted alarm pheromone varies in the relationship between
 total and relative amount of the putative two components, decyl acetate
 (DAc) and dodecyl acetate (DDAc). When pheromone is excreted with a
 predator present but not attacking, the percentage DDAc increases with the
 total amount of pheromone. When a predator does attack, however, the
 relationship between percentage DDAc and total amount of pheromone is
 reversed. Taken together, the alarm signal of thrips larvae appears to be
 context dependent, which to our knowledge is the first report of
 context-dependent composition of an alarm pheromone.
description: data context-dependent
 signalling in an insectExcel file with the data
 of the total amount of alarm pheromone and the relative amounts of its two
 compounds (as explained in further detail in the Excel file); there is a
 separate sheet for each of the five treatments.data.xlsx
DOI: 10.5061/dryad.m2db0
title: Data from: Pine afforestation decreases the long-term performance of understory shrubs in a semiarid Mediterranean ecosystem: a stable isotope approach.

description: 1. Plant–plant interactions shape the structure and composition of plant
 communities, but shifts in interaction outcomes might occur in the face of
 ongoing climate change. 2. We assessed the influence of Pinus halepensis
 plantations on the long-term ecophysiological performance of understorey
 vegetation, by conducting a retrospective comparison (1989–2007) of
 growth-ring widths, δ13C and δ18O between Rhamnus lycioides shrubs from
 two contrasting vegetation types: P. halepensis plantations vs. open
 woodlands. We also measured the leaf δ13C, δ18O, δ15N, and nutrient
 concentrations of understorey R. lycioides shrubs growing at varying
 distances from planted trees within pine plantations. 3. Dendroecological
 and stable isotope data revealed strong competitive effects of planted P.
 halepensis trees on R. lyciodies. Shrubs in pine plantations showed lower
 radial growth and higher growth ring δ13C and δ18O than those in open
 woodlands, indicating lower stomatal conductance and photosynthesis in the
 former. The strong competitive effects of P. halepensis on understorey R.
 lycioides were most evident in wet, productive years. Conversely, in very
 dry years, there were indications of a facilitative effect of planted P.
 halepensis canopies on understorey shrubs. 4. Within pine plantations,
 understorey R. lycioides shrubs growing at shorter distances from planted
 trees were forced to rely on more superficial and ephemeral soil water
 sources, which reduced their stomatal conductance (higher leaf δ18O) and
 interfered with nutrient uptake (lower leaf N and P concentrations and
 more negative δ15N). 5. The intrinsic water use efficiency of R. lycioides
 shrubs growing in open woodlands has increased during recent decades as a
 result of their ability to adjust their stomatal conductance in response
 to increasing temperature and atmospheric CO2. However, this adaptive
 response was much weaker or absent in the severely drought-stressed shrubs
 from pine plantations. 6. Pine afforestation strongly reduces water and
 nutrient availability for understorey shrubs in drylands, with potential
 long-term consequences for ecosystem biodiversity, structure and
 functioning. Competition by P. halepensis on R. lycioides clearly
 outweighed facilitation in the long-term, thus compromising the ability of
 understorey shrubs in semi-arid pine plantations to cope with climate
 change.
description: Rhamnus lycioides
 DDBBRhamnus
 DDBB.rar
DOI: 10.5061/dryad.pk31jt2
title: Data from: Low incidence of choroidal neovascularization following subthreshold diode micropulse laser (SDM) in high-risk AMD

description: Purpose: To determine the incidence of new choroidal neovascularization
 (CNV) in eyes with dry age-related macular degeneration (AMD) following
 subthreshold diode micropulse laser (SDM). Method: In an observational
 retrospective cohort study, the records of all patients active in the
 electronic medical records database were reviewed to identify eyes with
 dry AMD treated with SDM. Identified eyes were classified by simplified
 AREDS categories, and analyzed for the primary endpoint of new CNV after
 treatment. Results: The EMR revealed SDM was offered to 373/392 (95%)
 patients with dry AMD and elected by 363/373 (97%) between 2008-2017.
 Follow up was available for 354/363 patients (547 eyes, 98%) (range 6-108
 mos., avg. 22). CNV risk factors included age (median 84 years, 67%
 &gt; 80); reticular pseudodrusen (214 eyes, 39%); AREDS category (78%
 category 3 and 4); and fellow eye CNV (128 eyes, 23%). New CNV developed
 in 9/547 eyes (1.6%, annualized rate 0.87%). Visual acuity was unchanged.
 There were no adverse treatment effects. Summary: In a review of a large
 group of eyes with exceptionally high-risk AMD, SDM was followed by a very
 low incidence of new CNV. If confirmed by further study, SDM would offer a
 new and highly effective treatment to reduce the risk of vision loss from
 AMD.
description: CNV study Updated Excel
 DryadRaw data minus sex,
 notes, and name column
DOI: 10.5061/dryad.69f5vh2
title: Data from: Rock climbing activity and physical habitat attributes impact avian community diversity in cliff environments

description: As the sport of outdoor rock climbing rapidly grows, there is increasing
 pressure to understand how it can affect communities of organisms in cliff
 habitats. To that end, we surveyed 32 cliff sites in Boulder, Colorado,
 USA, and assessed the relative roles of human recreation and natural
 habitat features as drivers of bird diversity and activity. We detected
 only native avian species during our observations. Whereas avian abundance
 was not affected by climbing, avian species diversity and community
 conservation value were higher at low-use climbing formations. Models
 indicated that climber presence and cliff aspect were important predictors
 of both avian diversity and avian cliff use within our study area, while
 long-term climbing use frequency has a smaller, but still negative
 association with conservation value and cliff use by birds in the area. In
 contrast, the diversity of species on the cliff itself was not affected by
 any of our measured factors. To assess additional community dynamics, we
 surveyed vegetation and arthropods at ten site pairs. Climbing negatively
 affected lichen communities, but did not significantly affect other
 vegetation metrics or arthropods. We found no correlations between avian
 diversity and diversity of either vegetation or arthropods. Avian cliff
 use rate was positively correlated with arthropod biomass. We conclude
 that while rock climbing is associated with lower community diversity at
 cliffs, some common cliff-dwelling birds, arthropods and plants appear to
 be tolerant of climbing activity. An abiotic factor, cliff aspect strongly
 affected patterns of both avian diversity and cliff use, suggesting that
 the negative effects of rock climbing may be mitigated by informed
 management of cliff habitat that considers multiple site features.
description: avian_cliff_communities_datasetData was collected at rock climbing formations in Boulder, CO in 2015. Please view the README for more details.
DOI: 10.5061/dryad.040mt
title: Data from: Habitat context influences nitrogen removal by restored oyster reefs

description: 1. Like many ecosystem functions in marine and terrestrial environments,
 nutrient processing varies dramatically over small spatial scales, making
 efforts to apply findings within and across ecosystems challenging. In
 estuaries, information on the influence of habitat context on sediment
 nutrient cycling is lacking even though this is an important estuarine
 function with high societal value. 2. We collected triplicate intact
 sediment cores from restored oyster reefs located in different habitat
 contexts (adjacent to salt marshes, seagrass beds, and mudflats), as well
 as salt marshes, seagrass beds, and mudflats without reefs (controls).
 Sediment denitrification and fluxes of dissolved inorganic nitrogen were
 measured under ambient and experimentally elevated water column nitrate
 levels. 3. Under ambient nitrate, oyster reefs enhanced sediment
 denitrification by 18–275% over the controls, with highest rates of
 denitrification in the mudflat context. With experimentally elevated
 nitrate, the rate of denitrification was higher for oyster reefs compared
 to the controls in all contexts. This suggests that oyster reefs prime
 sediments to denitrify nitrate pulses by providing a labile carbon source
 for denitrifying bacteria. 4. There was a weak positive relationship
 between oyster density and denitrification under ambient nitrate
 concentrations and a positive relationship with denitrification that
 became negative beyond ~2400 individuals m−2 with elevated nitrate
 concentrations. The effect of the oyster reef on sediment denitrification
 was most pronounced in the mudflat context, due to the absence of other
 structured habitats and higher oyster density, compared to the other two
 habitat contexts investigated. 5. The consistency of denitrification
 efficiency across the habitats and lack of difference between habitats
 with reefs and those without (controls) suggests oyster-mediated
 denitrification is an effective sink for nitrogen in coastal systems. 6.
 Synthesis and applications. Our study indicates that oyster-mediated
 denitrification is dependent on the habitat context of the oyster reef,
 and variation in oyster density and the relative functional redundancy of
 oyster reefs where other structured habitats exist (e.g. seagrass and salt
 marshes) may explain this pattern. Efforts to model and predict ecosystem
 services provided through oyster reef restoration such as the removal of
 anthropogenically-derived nitrogen should incorporate how habitat context
 influences ecosystem functions.
description: Smyth et al JAPPL
 2014-00741Sediment fluxes, oyster
 reef density and size distribution, water quality parameters and study
 locations.
DOI: 10.5061/dryad.vn8km
title: Data from: Rapid and inexpensive whole-genome genotyping-by-sequencing for crossover localization and fine-scale genetic mapping.

description: The reshuffling of existing genetic variation during meiosis is important
 both during evolution and in breeding. The reassortment of genetic
 variants relies on the formation of crossovers (COs) between homologous
 chromosomes. The pattern of genome-wide CO distributions can be rapidly
 and precisely established by the short-read sequencing of individuals from
 F2 populations, which in turn are useful for quantitative trait locus
 (QTL) mapping. Although sequencing costs have decreased precipitously in
 recent years, the costs of library preparation for hundreds of individuals
 have remained high. To enable rapid and inexpensive CO detection and QTL
 mapping using low-coverage whole-genome sequencing of large mapping
 populations, we have developed a new method for library preparation along
 with Trained Individual GenomE Reconstruction, a probabilistic method for
 genotype and CO predictions for recombinant individuals. In an example
 case with hundreds of F2 individuals from two Arabidopsis thaliana
 accessions, we resolved most CO breakpoints to within 2 kb and reduced a
 major flowering time QTL to a 9-kb interval. In addition, an extended
 region of unusually low recombination revealed a 1.8-Mb inversion
 polymorphism on the long arm of chromosome 4. We observed no significant
 differences in the frequency and distribution of COs between F2
 individuals with and without a functional copy of the DNA helicase gene
 RECQ4A. In summary, we present a new, cost-efficient method for
 large-scale, high-precision genotyping-by-sequencing.
description: List of chromosomes and
 crossover positions for the wt populationThis is a tab-delimited
 text files with the format 
 
 .WT.refined.breaks.AB.txtList of crossover positions for the recq4a mutant populationThis is a tab-delimited text file with the format .MUT.refined.breaks.AB.txt