cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hqbzkh1jg
title: Universal temperature sensitivity of denitrification nitrogen losses in forest soils

description: Soil nitrous oxide (N2O) and dinitrogen (N2) emissions from
 denitrification are crucial to the global nitrogen (N)
 cycle. However, the temperature sensitivities of gaseous N losses
 in forest soils are poorly understood, limiting our ability to predict N
 cycling responses to global warming. We quantified temperature
 sensitivities (Q10) of denitrification-derived potential N2O and
 N2 production ex-situ for 18 forest soils across China.
 N2O and N2 production rates increased exponentially with
 temperature, showing large variation among soils. By contrast, the
 Q10 values for N2O (2.1±0.5) and N2 (2.6±0.6) were
 surprisingly similar across soils. N2 was more sensitive to temperature
 than N2O, suggesting warming could promote complete denitrification. The
 Q10 values for denitrification (2.3±0.5) were similar to
 those reported for aquatic sediments. Collectively, our results indicate a
 universal temperature sensitivity of gaseous N losses from
 denitrification, which will facilitate modelling N losses in response to
 warming on the global scale. 
description: We conducted laboratory incubation experiments with soils from 18
 forest sites across China along a 4000 km south-north transect spanning a
 33° latitudinal range. The soils were anaerobically incubated between 5
 and 35°C for 12 h after amending them with
 Na<sup>15</sup>NO<sub>3</sub> (99.26 atom%). Next,
 the production of N<sub>2</sub>O and
 N<sub>2</sub> as well as the consumption of
 nitrate (NO<sub>3</sub>-) were measured. In addition, we also
 measured several chemical and biological soil variables of potential
 importance for denitrification, such as pH, C/N ratio, water extractable
 organic carbon (WEOC), and functional genes
 (<em>nirK, nirS, nosZ</em>) abundance associated with gaseous
 N production.
DOI: 10.5061/dryad.4mw6m90cr
title: Dataset for: Aboveground carbon stocks, woody and litter productivity along an elevational gradient in the Rwenzori Mountains, Uganda

description: Montane forests are characterized by high biodiversity, endemism and
 strong elevational environmental gradients. The latter attribute makes
 them also suitable as a ‘natural laboratory’ for studying the effects of
 environmental parameters on ecosystem functions. To provide better insight
 into the carbon cycle of Afromontane ecosystems, we used an elevational
 gradient approach to quantify carbon stocks, woody and litter
 productivity, and their constraining factors. Twenty plots were
 established, covering five elevations from Kibale Forest at 1250 m to 3000
 m in the Rwenzori Mountains. Results revealed aboveground carbon stocks of
 between 185.4 ± 48.9 Mg C ha-1 and 70.8 ±18.6 Mg C ha-1 at 1250-1300 m and
 2700-3000 m respectively. Aboveground carbon tended to decrease with
 elevation, but this trend was not significant. This was due to
 similarities in stem diameter combined with different effects of tree
 height and stem density. Similarly, woody productivity did not change with
 elevation, ranging from 8.3 ± 4.1 Mg C ha-1 year-1 to 3.4 ± 1.5 Mg C ha-1
 year-1 at 2500-2600 m and 2700-3000 m respectively. However, litter
 productivity decreased linearly by 0.14 ± 0.04 Mg C ha-1 year-1 per 100 m
 of elevation increase, ranging from 4.0 ± 0.7 Mg C ha-1 year-1 at
 1750-1850 m to 1.2 Mg C ha-1 year-1 at 2700-3000 m. Topsoil
 physicochemical properties varied with elevation, but showed no
 significant relationship with carbon stocks and woody productivity.
 However, litter productivity increased with mean soil temperature, whereas
 it decreased with soil total nitrogen.
description: Raw data collected from the field. Plot level average values were
 then computed.
DOI: 10.5061/dryad.g1jwstqt3
title: Broad- and small-scale environmental gradients drive variation in chemical, but not morphological, leaf traits of vascular epiphytes

description: Variation in leaf functional traits along environmental gradients can
 reveal how vascular epiphytes respond to broad- and small-scale
 environmental gradients. Along elevational gradients, both temperature and
 precipitation likely play an important role as drivers of leaf trait
 variation, but these traits may also respond to small-scale changes in
 light, temperature, and humidity along the vertical environmental gradient
 within forest canopies. However, the relative importance of broad- and
 small-scale environmental gradients as drivers of variation in leaf
 functional traits of vascular epiphytes is poorly understood. Here, we
 examined variation in morphological and chemical leaf traits of 102
 vascular epiphyte species spanning two environmental gradients along Cofre
 de Perote mountain in Mexico: i) a broad-scale environmental gradient
 approximated by elevation as well as by species’ lower and upper
 elevational limits, and ii) small-scale environmental gradients using the
 relative height of attachment of an epiphyte on a host tree as a proxy for
 variation in environmental conditions within the forest canopy. We also
 assessed whether variation in morphological and chemical leaf traits along
 these gradients were consistent across photosynthetic pathways (CAM and
 C3). Broad- and small-scale environmental gradients explained more
 variation in chemical traits (marginal R2: 11-89%) than in morphological
 traits (marginal R2: 2-31%). For example, leaf carbon isotope signatures
 (δ13C), which reflects water-use efficiency, varied systematically across
 both environmental gradients, suggesting a decrease in water-use
 efficiency with increasing lower and upper elevational limits and an
 increase in water-use efficiency with relative height of attachment. The
 influence of lower and upper elevational limits on trait variation
 differed between photosynthetic pathways, except for leaf dry matter
 content and leaf nitrogen-to-phosphorus ratio. Contrary to our
 expectations, broad- and small-scale environmental gradients explained
 minimal variation in morphological leaf traits, suggesting that
 environmental conditions do not constrain morphological leaf trait values
 of vascular epiphytes. Our findings suggest that assessing multiple
 drivers of leaf trait variation among photosynthetic pathways is key for
 disentangling the mechanisms underlying responses of vascular epiphytes to
 environmental conditions.
DOI: 10.5061/dryad.3j9kd51mn
title: Data from: Hierarchical variation in phenotypic flexibility across timescales and associated survival selection shape the dynamics of partial seasonal migration

description: Population responses to environmental variation ultimately depend on
 within-individual and among-individual variation in labile phenotypic
 traits that affect fitness, and resulting episodes of selection. Yet,
 complex patterns of individual phenotypic variation arising within and
 between time periods, and associated variation in selection, have not been
 fully conceptualised or quantified. We highlight how structured patterns
 of phenotypic variation in dichotomous threshold traits can theoretically
 arise and experience varying forms of selection, shaping overall
 phenotypic dynamics. We then fit novel multistate models to ten years of
 band-resighting data from European shags to quantify phenotypic variation
 and selection in a key threshold trait underlying spatio-seasonal
 population dynamics: seasonal migration versus residence. First, we
 demonstrate substantial among-individual variation alongside substantial
 between-year individual repeatability in within-year phenotypic variation
 (‘flexibility’), with weak sexual dimorphism. Second, we demonstrate that
 between-year individual variation in within-year phenotypes
 (‘supraflexibility’) is structured and directional, consistent with the
 threshold trait model. Third, we demonstrate strong survival selection on
 within-year phenotypes, and hence on flexibility, that varies across years
 and sexes, including episodes of disruptive selection representing costs
 of flexibility. By quantitatively combining these results, we show how
 supraflexibility and survival selection on migratory flexibility jointly
 shape population-wide phenotypic dynamics of seasonal movement.
description: The present repository contains the dataset in ".csv"
 format (see details in 'README' file). A second repository
 contains the code for reading in this file and running the analyses (https://doi.org/10.5281/zenodo.6544485, hosted by Zenodo). A third repository contains supplementary files produced by the code for the main analyses, which include the complete model outputs and detailed numerical summaries (https://doi.org/10.5281/zenodo.6544487, hosted by Zenodo).
DOI: 10.5061/dryad.prr4xgxpd
title: Density-dependent selection and the maintenance of colour polymorphism in barn owls

description: The capacity of natural selection to generate adaptive changes is
 according to the Fundamental Theorem of Natural Selection proportional to
 the additive genetic variance in fitness. In spite of its importance for
 development of new adaptations to a changing environment, processes
 affecting the magnitude of the genetic variance in fitness-related traits
 are poorly understood. Here we show that the red-white colour polymorphism
 in female barn owls is subject to density-dependent selection at the
 phenotypic and genotypic level. The diallelic melanocortin-1 receptor
 (MC1R) gene explained a large amount of the phenotypic variance in reddish
 colouration in the females (R^2 = 59.8 %). Red individuals (RR genotype)
 were selected for at low densities, while white individuals (WW genotype)
 were favoured at high densities and were less sensitive to changes in
 density. We show that this density-dependent selection favours white
 individuals and predicts fixation of the white allele in this population
 at longer time scales without immigration or other selective forces.
 Still, fluctuating population density will cause selection to fluctuate
 and periodically favour red individuals. These results suggest how
 balancing selection caused by fluctuations in population density can be a
 general mechanism affecting the level of additive genetic variance in
 natural populations.
DOI: 10.5061/dryad.5tb2rbp67
title: Architectural effects regulate resource allocation within the inflorescences with nonlinear blooming patterns

description: These data were generated to investigate the resource allocation
 pattern within the inflorescence of Salvia przewalskii, a perennial herb
 with 4-ouvle ovary flowers and flowering sequence-floral position
 decoupled inflorescences. Spatial and temporal resource allocations within
 inflorescences have been well-studied in many plants based on
 flowering sequence or floral position. However, there
 have been few attempts to investigate architectural effects and
 resource competition in species where the blooming pattern does
 not follow a linear positional pattern within the inflorescence.
 Moreover, most flowering plants show female-biased sex allocation
 in early or basal flowers, but it is unclear in species with inherent
 and changeless ovule production. The data demonstrated that
 pollen production and dry mass deceased from bottom to top flowers but
 didn’t significantly differ following flowering sequence, resulting in
 male-biased sex allocation in basal flowers. The seed production, fruit
 set, bud developmental exhibited significant declining trends from
 proximal to distal positions regardless of the thinning and pollen
 treatments. Meanwhile, the seed production, fruit set, bud developmental
 success did not significant difference when thinning conducted according
 to flowering sequence. Thus, architectural effects plays a crucial role in
 resource allocation within decoupled flowering inflorescences. Moreover,
 the inherent floral traits, such as changeless ovule production, may
 modify architectural effects on sex allocation. 
description: All the data were collected from a natural population near the
 Shangri-La Alpine Botanical Garden, Yunnan Province, SW China (27°54′N,
 99°38′E, 3300-3350 m a.s.l), and carried out between July and August in
 six consecutive flowering seasons from 2016 to 2021. The pollen and ovule
 number were counted in the lab with a microscope. The flower number and
 flower longevity per flower were recorded from several plants in a natural
 population. The flower length were measured by digital calipers in each
 inflorescence. The dry biomass per flower was weighed to the nearest 0.01
 mg after dried at 80°C (24 h). In addition, all fruits per inflorescence
 were collected at the end of the fruiting season (~30 days after flower
 wilting), the seed production, fruit set, and bud developmental success
 per position or blooming stage were counted at lab.
DOI: 10.5061/dryad.xpnvx0kj1
title: Ancient sedimentary plant DNA dataset from Batagay (B17), Yakutia

description: Here we provide a dataset on genetic plant diversity retrieved from
 permafrost sedimentary ancient DNA (sedaDNA) of the Batagay megaslump,
 Yakutia. Our dataset encompasses sedaDNA sequence data of 10 sediment
 samples. We used a PCR-based metabarcoding approach combined with
 Next-Generation Sequencing to assess the past, local vegetation
 compositional changes around the megaslump. As a plant specific
 metabarcode we applied the established chloroplastidal P6 loop trnL marker
 for plant diversity assessment. PCR products were sequenced on one
 Illumina sequencing HiSeq 2500 run.
description: We extracted sedimentary DNA from the permafrost samples using
 the DNeasy PowerMax Soil Kit. We used a PCR-based metabarcoding approach
 combined with Next-Generation Sequencing. As a plant specific metabarcode
 we applied the established chloroplastidal P6 loop trnL marker for plant
 diversity assessment and amplified plant DNA from sedimentary DNA
 extracts. Resulting PCR products were replicated 3 times for each sample,
 which were sequenced on one Illumina sequencing run. The underlying data
 set consists of raw R1.fastq and R2.fastq files of the sequencing run, two
 scripts that explain how to use the OBITools pipeline for data analyses
 and how to prepare taxonomic databases with EcoPCR and OBITools, the
 tagfile needed for demultiplexing the sequence raw data into samples, two
 database files for taxonomic assignment and one final data
 files.
description: For
 reanalysis of data we provide the following data files:
 1. Illumina sequencing raw data of the sequencing run: ALRK-4.
 Data files are compressed. ALRK-4
 (190315_NB501473_A_L1-4_ALRK-4_R1.fastq,
 190315_NB501473_A_L1-4_ALRK-4_R2.fastq). 2. Two scripts
 to run the OBITools pipeline with a short description of each
 step. Data analyses with OBITools
 (Script_data_analyses_with_OBITools.txt) Database
 creation with EcoPCR and OBITools
 (Script_Database_creation_for_OBITools.txt) 3. Tagfiles
 needed for the OBITools pipeline with a corresponding file to associate
 the sample names in the tagfiles which indicate the sample batch number
 and corresponding controls (DNA extraction blank (BLANK) and PCR negative
 control (NTC)). ALRK-4: ALRK-4_tagfile.txt
 ALRK-4_names.txt 4. Taxonomic database files needed for
 the OBITools pipeline (see
 Script_data_analyses_with_OBITools.txt) EMBL database
 (g_h_embl138_final.uniqIDs.fasta) Arctic database
 (arctborbryo_gh.fasta, ecochange.zip) 5. Final data
 tables after bioinformatic analyses with OBITools. We provide the table
 with best taxonomic assignment. We the final name, we used the best name
 given by the database with the best identity score. If both databases were
 giving similar identity score, then we prioritise the arctic
 database. ALRK-4
 (ALRK-4_final_assignment.txt)
DOI: 10.5061/dryad.cfxpnvx7p
title: Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination

description: Conservation of thermally sensitive species depends on monitoring
 organismal and population-level responses to environmental change in real
 time. Epigenetic processes are increasingly recognized as key integrators
 of environmental conditions into developmentally plastic responses, and
 attendant epigenomic datasets hold potential for revealing cryptic
 phenotypes relevant to conservation efforts. Here, we demonstrate the
 utility of genome-wide DNA methylation (DNAm) patterns in the face of
 climate change for a group of especially vulnerable species, those with
 temperature-dependent sex determination (TSD). Due to their reliance on
 thermal cues during development to determine sexual fate, contemporary
 shifts in temperature are predicted to skew offspring sex ratios and
 ultimately destabilize sensitive populations. Using reduced-representation
 bisulfite sequencing, we profiled the DNA methylome in blood cells of
 hatchling American alligator (Alligator mississippiensis), a TSD species
 lacking reliable markers of sexual dimorphism in early life-stages. We
 identified 120 sex-associated differentially methylated cytosines (DMCs;
 FDR &lt; 0.1) in hatchlings incubated under a range of temperatures,
 as well as 707 unique temperature-associated DMCs. We further developed
 DNAm-based models capable of predicting hatchling sex with 100% accuracy
 (in 20 training samples and 4 test samples) and past incubation
 temperature with a mean absolute error of 1.2˚C (in 4 test samples) based
 on the methylation status of 20 and 24 loci, respectively. Though largely
 independent of epigenomic patterning occurring in the embryonic gonad
 during TSD, DNAm patterns in blood cells may serve as non-lethal markers
 of hatchling sex and past incubation conditions in conservation
 applications. These findings also raise intriguing questions regarding
 tissue-specific epigenomic patterning in the context of developmental
 plasticity.
DOI: 10.5061/dryad.dv41ns219
title: Territory-level temperature influences breeding phenology and reproductive output in three forest passerine birds

description: Temperature plays an important role in determining the breeding phenology
 of birds in temperate climates, with higher spring temperatures associated
 with earlier breeding. However, the effect of localised territory-scale
 temperature variations is poorly understood, with relationships between
 temperature and breeding phenology mostly studied using coarse-grained
 climatic indices. Here, we interpolate spring temperatures recorded at 150
 m2 grid intersections encompassing 417 ha of forest to examine the
 influence of territory-scale temperature, and its interaction with mean
 annual temperature, on territory selection, breeding phenology, clutch
 size and fledging success for three co-occurring single-brooded passerine
 birds using data from 672 nests over four years. All species exhibited
 significant trends in reproductive traits associated with territory-scale
 temperature. Pied flycatchers Ficedula hypoleuca settled in cooler
 territories first, where they raised more fledglings. Blue tits Cyanistes
 caeruleus laid larger clutches in warmer territories in warm years and
 always laid earlier at warmer territories irrespective of annual
 temperature variation. Contrastingly, pied flycatcher and wood warbler
 Phylloscopus sibilatrix breeding phenology was earlier at warmer
 territories in cool years and cooler territories in warm years, with wood
 warbler clutch size responding similarly to this interaction. Greater
 previous breeding experience and increased higher rates of historical
 territory occupancy (territory quality) also predicted earlier breeding
 phenology and higher fledging success for pied flycatchers. We suggest
 that the migratory pied flycatcher and wood warbler are best synchronised
 with their prey availability in cooler years at a local population level.
 However resident blue tits match local phenology across all years, which
 is potentially advantageous under warmer predicted climate change
 scenarios. We conclude that temperature at the territory scale can be an
 important driver of settlement and breeding phenology and influence
 reproductive traits.
description: All details are contained in the methods section of the
 associated Oikos manuscript.
description: Species: PIEFL =
 Pied Flycatcher, BLUTI = Blue Tit, WOOWA = Wood
 Warbler.  
 NestboxID for WOOWA
 purely a nest location marker and not a nestbox as this species is a
 ground nester, this value therefore specific to individual
 nests.  
 BrEx = Breeding
 Experience.  
 MC = Mean
 Centred.   NA values indicate that data was not
 collected for this particular value.
 In PIEFL parental
 ID NA means that this individual was not caught and identified rather than
 not present. NumberFledged = NA for predated
 broods rather than 0, as these were removed from analyses at this
 stage.   All other relevant dataset
 information is contained within the associated Oikos
 manuscript.
DOI: 10.5061/dryad.w6m905qrs
title: Differential nutrient limitation and tree height control leaf physiology, supporting niche partitioning in tropical dipterocarp forests

description: Revealing the mechanisms of environmental niche partitioning within
 lowland tropical forests is important for understanding the drivers of
 current species distributions and potential vulnerability to environmental
 change. Tropical forest structure and species composition change across
 edaphic gradients in Borneo over short distances. However, our
 understanding of how edaphic conditions affect tree physiology and whether
 these relationships drive niche partitioning within Bornean forests
 remains incomplete. This study evaluated how leaf physiological function
 changes with nutrient availability across a fine-scale edaphic gradient
 and whether these relationships vary according to tree height.
 Furthermore, we tested whether intraspecific leaf trait variation allows
 generalist species to populate a wider range of environments. We measured
 leaf traits of 218 trees ranging in height from 4 to 66 m from 13
 dipterocarp species within four tropical forest types (alluvial, mudstone,
 sandstone, kerangas) occurring along an &lt; 5km edaphic gradient in
 North Borneo. The traits measured included saturating photosynthesis
 (Asat), maximum photosynthetic capacity (Vcmax), leaf dark respiration
 (Rleaf), leaf mass per area (LMA), leaf thickness, minimum stomatal
 conductance (gdark) and leaf nutrient concentrations (N, P, Ca, K, Mg).
 Across all species, leaf traits varied consistently in response to soil
 nutrient availability across forest types except Rleaf_mass, [Mg]leaf and
 [Ca]leaf. Changes in photosynthesis and respiration rates were related to
 different leaf nutrients across forest types, with greater nutrient-use
 efficiency in more nutrient-poor environments. Generalist species
 partially or fully compensated reductions in mass-based photosynthesis
 through increasing LMA in more nutrient-poor environments. Leaf traits
 also varied with tree height, except Vcmax_mass, but only in response to
 height-related modifications of leaf morphology (LMA and leaf thickness).
 These height-trait relationships did not vary across the edaphic gradient,
 except for Asat, [N]leaf, [P]leaf and [K]leaf. Our results highlight that
 modification of leaf physiological function and morphology act as
 important adaptations for Bornean dipterocarps in response to edaphic and
 vertical environmental gradients. Meanwhile, multiple nutrients appear to
 contribute to niche partitioning and could drive species distributions and
 high biodiversity within Bornean forest landscapes.