cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t78400r
title: Data from: A full annual perspective on sex-biased migration timing in long-distance migratory birds

description: In many taxa, the most common form of sex-biased migration timing is
 protandry – the earlier arrival of males at breeding areas. Here we test
 this concept across the annual cycle of long-distance migratory birds.
 Using more than 350 migration tracks of small-bodied trans-Saharan
 migrants, we quantify differences in male and female migration schedules
 and test for proximate determinants of sex-specific timing. In spring,
 males on average departed from the African non-breeding sites about 3 days
 earlier and reached breeding sites ca. 4 days ahead of females. In autumn,
 males started migration about 2 days earlier, but this difference did not
 carry-over to arrival at the non-breeding sites. A cross-species
 comparison revealed large variation in the level of protandry and
 protogyny across the annual cycle. While we found tight links between
 individual timing of departure and arrival within each migration season,
 only for males the timing of spring migration was linked to the timing of
 previous autumn migration. In conclusion, our results demonstrate that
 protandry is not exclusively a reproductive strategy but rather occurs
 year-round and the two main proximate determinants for the magnitude of
 sex-biased arrival times in autumn and spring are sex-specific differences
 in departure timing and migration duration.
description: Sex-biased migration
 timing in 14 Afro-Palearctic migratory birdsdatabase_submission.csv
DOI: 10.5061/dryad.30h50r7
title: Data from: Global patterns in fine root decomposition: climate, chemistry, mycorrhizal association, and woodiness

description: Fine root decomposition constitutes a critical yet poorly understood flux
 of carbon and nutrients in terrestrial ecosystems. Here, we present the
 first large‐scale synthesis of species trait effects on the early stages
 of fine root decomposition at both global and local scales. Based on
 decomposition rates for 279 plant species across 105 studies and 176
 sites, we found that mycorrhizal association and woodiness are the best
 categorical traits for predicting rates of fine root decomposition.
 Consistent positive effects of nitrogen and phosphorus concentrations and
 negative effects of lignin concentration emerged on decomposition rates
 within sites. Similar relationships were present across sites, along with
 positive effects of temperature and moisture. Calcium was not consistently
 related to decomposition rate at either scale. While the chemical drivers
 of fine root decomposition parallel those of leaf decomposition, our
 results indicate that the best plant functional groups for predicting fine
 root decomposition differ from those predicting leaf decomposition.
description: Fine root decomposition
 ratesRootDecomp.xlsx
DOI: 10.5061/dryad.rh6h5d0
title: Data from: Deterministic tropical tree community turnover: evidence from patterns of functional beta diversity along an elevational gradient

description: Explaining the mechanisms that produce the enormous diversity within and
 between tropical tree communities is a pressing challenge for plant
 community ecologists. Mechanistic hypotheses range from niche-based
 deterministic to dispersal-based stochastic models. Strong tests of these
 hypotheses require detailed information regarding the functional
 strategies of species. A few tropical studies to date have examined trait
 dispersion within individual forest plots using species trait means in
 order to ask whether coexisting species tend to be more or less
 functionally similar than expected given a null model. The present work
 takes an alternative approach by: (i) explicitly incorporating
 population-level trait variability; and (ii) quantifying the functional
 beta diversity in a series of 15 tropical forest plots arrayed along an
 elevational gradient. The results show a strong pattern of decay in
 community functional similarity with elevation. These observed patterns of
 functional beta diversity are shown to be highly non-random and support a
 deterministic model of tropical tree community assembly and turnover.
description: SwensonEtAl.2011.traitsSpecies level trait values for Swenson et al. 2011 PRSB study. Units for traits are given in column headers. Six letter species codes are given in first column, which are the codes consistent with those used in the Luquillo LTER site for plant species.
DOI: 10.5061/dryad.5jh21k3
title: Data from: Historical population size change and differentiation of relict populations of the endangered giant kangaroo rat

description: From a conservation management perspective it is important to understand
 how genetic diversity is partitioned across a species’ range, including
 (1) identification of evolutionarily distinct units versus those recently
 isolated through anthropogenic activities and (2) the relative genetic
 contributions among components of fragmented (meta)populations. To address
 these questions, we investigated the phylogeography and metapopulation
 structure among relict populations of the endangered giant kangaroo rat
 (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem.
 This keystone species underwent a ~97% range reduction over the past
 century, resulting in a current range that is highly fragmented, with two
 dominant northern and southern populations occurring 150 km apart. We
 sequenced &gt;800 bp of mitochondrial DNA and genotyped 17 nuclear
 microsatellites in &gt;275 D. ingens to assess the evolutionary
 relationship of these populations as well as the genetic structure within
 the northern metapopulation. A Bayesian Skyline Plot indicated that the
 species experienced a demographic expansion toward the end of the
 Pleistocene, with a recent population decline. Northern and southern D.
 ingens split 1,857–13,443 years ago, prior to the massive conversion of
 the San Joaquin Valley to irrigated agriculture. We recommend that the
 northern and southern populations of D. ingens be re-classified as
 distinct population segments under the United States Endangered Species
 Act. We also observed population structure and asymmetrical migration
 within northern D. ingens where the Tumey Hills acted as a source
 contributing gene flow to all peripheral populations. This emphasized the
 importance of this location in the conservation of the metapopulation as a
 whole.
description: Statham_Giant_kangaroo_rat_submission_DryadSequence and genotype data for giant kangaroo rats (Dipodomys ingens). The file has three tabs, the first of which is named 'read me' and describes the contents of the other tabs.
DOI: 10.5061/dryad.7kc589v
title: Data from: The effects of Bacillus subtilis on Caenorhabditis elegans fitness after heat stress

description: Microbes can provide their hosts with protection from biotic and abiotic
 factors. While many studies have examined how certain bacteria can
 increase host lifespan, fewer studies have examined how host reproduction
 can be altered. The nematode Caenorhabditis elegans has been a
 particularly useful model system to examine how bacteria affect the
 fitness of their hosts under different contexts. Here, we examine how the
 bacterium Bacillus subtilis, compared to the standard C. elegans lab diet,
 Escherichia coli, affects C. elegans survival and reproduction after
 experiencing a period of intense heat stress. We find that under standard
 conditions, nematodes reared on B. subtilis produce fewer offspring than
 when reared on E. coli. However, despite greater mortality rates on B.
 subtilis after heat shock, young adult nematodes produced more offspring
 after heat shock when fed B. subtilis compared to E. coli. Because
 offspring production is necessary for host population growth and
 evolution, the reproductive advantage conferred by B. subtilis supersedes
 the survival advantage of E. coli. Furthermore, we found that nematodes
 must be reared on B. subtilis (particularly at the early stages of
 development) and not merely be exposed to the bacterium during heat shock,
 to obtain the reproductive benefits provided by B. subtilis. Taken
 together, our findings lend insight into the importance of environmental
 context and interaction timing in shaping the protective benefits
 conferred by a microbe toward its host.
description: Figure
 3Nematodes were reared on
 E. coli OP50 until L4/young adult stage (at about three days old), then
 subsequently transferred to the indicated bacterium. They were heat
 shocked at 34˚C three days later. After three and six hours, replicate
 plates were removed from the heat and scored for
 survival180427 mechanism of increased
 fecundity post-HS.xlsxFigure
 4Nematodes were reared on
 the indicated bacterium until three days old, then were either left at
 standard conditions or heat shocked. To quantify offspring, we washed
 worms off plates with M9 into 1.5ml tubes ("total volume"
 indicates volume of liquid in the tube). Then we aliquoted 10ul from each
 tube three times onto glass wells, took the mean of the three aliquots,
 then multiple by the total volume of each tube, to estimate the number of
 offspring in each tube.180330 168 vs nos vs
 OP50.xlsxFigure
 5Nematodes were reared on
 the first bacterium indicated before being transferred to the bacterium
 they were heat shocked on when they reached adulthood180220 exposure time pt.
 2.xlsxFigure
 6Nematodes were
 transferred to each bacterium as indicated each day before being heat
 shocked on day 4180829 exposure time refined
 for hot worms 1 repeat.xlsx
DOI: 10.7927/4q5z-bm48
title: IPCC AR6 Synthesis Report LR Figure 3.2 (c1): Impact of projected global warming levels on maize yield

description: Changes in maize yield at projected global warming levels (GWLs) of 1.6°C–2.4o C (2.0°C), 3.3°C–4.8o C (4.1°C) and 3.9°C–6.0o C (4.9°C). Median yield changes from an ensemble of 12 crop models, each driven by bias-adjusted outputs from 5 Earth system models from the Agricultural Model Intercomparison and Improvement Project (AgMIP) and the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP). Maps depict 2080–2099 compared to 1986–2005 for current growing regions (more than 10 ha), with the corresponding range of future global warming levels shown under SSP1-2.6, SSP3-7.0 and SSP5-8.5, respectively. Hatching indicates areas where less than 70% of the climate-crop model combinations agree on the sign of impact.
DOI: 10.5061/dryad.sj3m45m
title: Data from: An artificial habitat facilitates a climate-mediated range expansion into a suboptimal novel ecosystem

description: [No abstract entered]
description: Distribution Survey
 DataPresence/absence of A.
 pisonii during distribution surveysCrab Size
 DataSizes of all A. pisonii
 measured throughout study.Cold Tolerance
 DataData from cold tolerance
 experiment including temperature of death of each crab.Relative Abundance
 DataData from relative
 abundance study. Relative abundance of A. pisonii are expressed in Catch
 per Unit Effort (CPUE) in crabs caught per minute.Lethal Temperature
 Logger DataThermal logger data used
 to determine the number of days and hours spent under the lethal
 temperature 50 (LT50) and complete lethal temperature (LT100) of A.
 pisonii in each habitat and site.Minimum Temperature
 Logger DataDaily minimum
 temperatures recorded by thermal loggers each day at each site in each
 habitat.
DOI: 10.5061/dryad.r51rh2s
title: Data from: Optical and molecular signatures of dissolved organic matter reflect anthropogenic influence in a coastal river, Northeast China

description: Sources and molecular composition of dissolved organic matter (DOM) in
 coastal rivers have been tightly linked with its reactivity and fate, thus
 influencing element and nutrient cycling. The DOM in coastal rivers is
 usually sourced from both terrestrial and marine inputs, with further
 complication by anthropogenic activities, which is less understood in
 coastal rivers located near populated industrial regions. In this study,
 DOM in a typical anthropogenically influenced coastal river, Daliao River,
 was analyzed for optical analyses and for molecular composition via
 Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to
 give a better scope of composition and sources of DOM. The DOM was
 enriched in autochthonous and anthropogenic inputs at upstream sites
 according to high chlorophyll a concentrations, strong protein-like
 fluorescence, and nonoxygen heteroatomic CHOS formulae (19–24% by relative
 peak intensity) detected by FT-ICR MS analysis. A series of
 surfactant-like formulae, indicative of wastewater inputs, were identified
 and showed a decreasing trend from upstream to the river mouth. Compared
 with large world rivers, the DOM of Daliao River is characterized by
 higher abundances of heteroatomic (excluding O) formulae and molecular
 lability, which is likely caused by strong autochthonous and anthropogenic
 inputs. In general, we demonstrate that in addition to optical properties,
 the molecular composition can assess the specific anthropogenic imprints
 and molecular lability of DOM, which is essential for constraining sources
 and identifying processes during the transit of DOM from the river to
 estuary with increasing urbanization and industrialization.
description: Daliao River unique
 molecular formulae obtained from FT-ICR MSThe 8889 unique
 molecular formulae of six Daliao River samples (DL1 to DL6) obtained from
 FT-ICR MS. For more information, please contact D. He
 (dinghe@zju.edu.cn).
DOI: 10.5061/dryad.11d0f29
title: Data from: A macroecological approach to evolutionary rescue and adaptation to climate change

description: Despite the widespread use of Ecological Niche Models (ENMs) for
 predicting the responses of species to climate change, these models do not
 explicitly incorporate any population-level mechanism. On the other hand,
 mechanistic models adding population processes (e.g., biotic interactions,
 dispersal and adaptive potential to abiotic constraints) are much more
 complex and difficult to parameterize, especially if the goal is to
 predict range shifts for many species simultaneously. In particular, the
 adaptive potential (based on genetic adaptations, phenotypic plasticity
 and behavioral adjustments for physiological responses) of local
 populations has been the less studied mechanism affecting species’
 responses to climatic change so far. Here, we discuss and apply an
 alternative macroecological framework to evaluate the potential role of
 evolutionary rescue under climate change based on ENMs. We begin by
 reviewing eco-evolutionary models that evaluate the maximum sustainable
 evolutionary rate under a scenario of environmental change, showing how
 they can be used to understand the impact of temperature change on a
 Neotropical anuran species, the Schneider’s toad Rhinella diptycha. Then
 we show how to evaluate spatial patterns of species’ geographic range
 shift using such models, by estimating evolutionary rates at the species’
 trailing edge distribution estimated by ENMs and by recalculating the
 relative amount of total range loss under climate change. We show how
 different models can reduce the expected range loss predicted for the
 studied species by potential ecophysiological adaptations in some regions
 of the trailing edge predicted by ENMs. For general applications, we
 believe that parameters for large numbers of species and populations can
 be obtained from macroecological generalizations (e.g. allometric
 equations and ecogeographical rules), so our framework coupling ENMs with
 eco-evolutionary models can be applied to achieve a more accurate picture
 of potential impacts from climate changes and other threats to
 biodiversity.
description: Rhinella_CCSM_Bio1_FINALMain data to be read by R-script and perform all analysesR-Script for DRYADR-script to do all geographical analyses in the paper
DOI: 10.5061/dryad.cn9908c
title: Data from: Richness of plant communities plays a larger role than climate in determining responses of species richness to climate change

description: 1. Experimental warming in situ suggests that warming could lead to a loss
 of biodiversity. However, species that remain in situ and experience
 climate change will interact with species tracking climate change, which
 could also affect patterns of biodiversity. The relative contribution of
 species gains and losses to net changes in species richness is still
 unclear. 2. We use transplanted plant communities to test the hypothesis
 that both the change in climate and ecological communities tracking
 climate change will influence how species richness responds to climate
 change. Three intact alpine plant communities were reciprocally
 transplanted to create scenarios in which species experienced warmer and
 wetter conditions (transferred to lower elevations) and cooler and drier
 conditions (transferred to higher elevations) over 10 years on the Tibetan
 Plateau. Communities transplanted into the same elevation as controls
 represent species tracking climate change. 3. Transferring to lower
 elevations generally caused a net increase in richness and a higher rate
 of gains relative to the control plots; the magnitude of this effect
 depended on the specific elevation. Transferring to higher elevations lead
 to either net increases or decreases in richness and gains, depending on
 elevation. Species gains predicted much more variation in changes in
 species richness (50%) than did species loss (9%). 4. Species richness at
 the receptor site and the donor site were both important predictors of
 variation in species richness, and the abiotic environment did not explain
 additional variation. Changes in cover of dominant plant species in
 response to transfers did not predict changes in species richness, species
 gain, or species loss. Our results suggest that species gains from species
 tracking climate change at the receptor sites, rather than species loss
 from the donor sites, predicted changes in species richness. 5. Synthesis.
 Warming experiments with physical barriers to dispersal may overestimate
 the negative effect of warming on plant diversity by not accounting for
 species gains. Our study highlights the importance of biotic factors in
 addition to the abiotic environment, when considering how climate change
 will affect plant diversity.
description: Plant species
 composition under reciprocal transplantion along elevation
 gradientThe data file is how
 response of plant species to warming and cooling when reciprocal
 transplantion along 3200-3800 m elevation gradient form 2007 to 2015 on
 the Tibetan Plateau.data to J
 Ecology.xlsx
DOI: 10.5281/zenodo.18390227
title: CDC_ILI
DOI: 10.5281/zenodo.18390228
title: CDC_ILI
DOI: 10.5061/dryad.2tf77nt
title: Data from: Hybridization among the species of Veronica subg. Pseudolysimachium from the Altai detected by SRAP markers

description: Veronica subg. Pseudolysimachium is widely known and cultivated because of
 the large and dense inflorescences of its species. Their success as
 cultivated plant stems in part to the cross-compatibility across the
 subgenus and in the part to the wide ecological amplitude from species
 growing in wetlands to others growing in semi-deserts. Hybridization
 between species is believed to be frequent due to the large morphological
 variation and intermediate forms in sympatry of their putative parents.
 The Russian Altai is a center of diversity for the taxon and many hybrid
 taxa have been described there based on morphology. Here, we test these
 hybrid hypotheses using dominant SRAP markers. The method relies on
 primers anchored in open reading frames and amplifying intronic regions,
 which are scored as fragment length polymorphisms. Using seven primer
 pairs, we analyzed 63 loci without missing data. Our data support a close
 relationship of V. × grisea, V. × schmakovii and V. taigischensis with V.
 longifolia but influence of the other suggested parents V. incana, V.
 porphyriana, and V. pinnata is weak. Similarly, V. × sessiliflora shows
 strong genetic similarity with V. porphyriana but only weakly with V.
 pinnata. Overall, the methodology worked reliably and provided a large
 number of variable polymorphisms. The lack of support for the hybrid
 hypotheses is, therefore, considered to be due to still low number of loci
 and possible backcrossing with one of the parents.
description: matrix of SRAP marker
 dataWe scored seven primer
 combinations o SRAP-primers, namely ME1-EM1; ME1-EM3; ME3-EM1; ME3-EM3;
 ME3-EM4; ME1-EM5; ME3-EM5. Forward primers me1,
 5'-TGAGTCCAAACCGGATA-3'; me2, 5'-TGAGTCCAAACCGGAGC-3';
 me3, 5'-TGAGTCCAAACCGGAAT-3'; me4,
 5'-TGAGTCCAAACCGGACC-3'; me5, 5'-TGAGTCCAAACCGGAAG-3'.
 The reverse primers were em1, 5′-GACTGCGTACGAATTAAT-3′; em2,
 5′-GACTGCGTACGAATTTGC-3′; em3, 5′-GACTGCGTACGAATTGAC-3′; em4,
 5′-GACTGCGTACGAATTTGA-3′; em5, 5′-GACTGCGTACGAATTAAC-3′. The resulting PCR
 products were checked on 2% agarose gel and visualized (after staining
 with ethidium bromide) under UV-light. To determine the length of DNA
 fragments a marker of known molecular weight (100 bp DNA Ladder) was run
 in parallel.matrix.xlsx
DOI: 10.5061/dryad.cd57c84
title: Data from: Growth of maize on mixed nitrate and ammonium promotes auxin synthesis and biomass accumulation

description: Mixed nitrate (NO3-) and ammonium (NH4+) as nitrogen source can improve
 plant growth. The underlying mechanism was explored by using metabolomics
 and transcriptome. Maize plants were grown hydroponically with three
 nitrogen forms (nitrate, 75/25 nitrate/ammonium and ammonium). Mixed N
 increased photosynthetic rate compared to nitrate supply, and had the
 highest leaf area, shoot and root biomass among the three nitrogen
 treatments. In shoot and root, the concentration of nitrogenous compounds
 (NH4+, Gln, Asn) and carbohydrates (sucrose, glucose, fructose) in plant
 with mixed N supply was higher than that with nitrate supply, but lower
 than that with ammonium supply. The activity of the related enzymes (GS,
 ASNS, PEPCase, invertase, AGPase) changed accordingly. Specifically, mixed
 N enhanced IAA synthesis via shikimic acid pathway, as indicated by the
 higher PEP and tryptophan compared to the other two treatments. The
 expression of corresponding genes involving IAA synthesis and response
 were up-regulated. Sole ammonium supply resulted in high level of Gln and
 Asn, starch, and T6P. It is concluded that, in addition to increase
 photosynthesis, mixed N supply enhances leaf growth via increasing IAA
 synthesis to build a big sink for C and N utilization, which, in turn,
 facilitates further C assimilation and N uptake.
description: Metabolites in the shoot
 and root identified by LC-MS under sole nitrate, 75/25 nitrate and
 ammonium ratio supply, and sole ammonium supply in 12d for maize (Zhengdan
 958) seedlings in hydroponic condition.Metabolites in the shoot
 and root identified by LC-MS under sole nitrate, 75/25 nitrate and
 ammonium ratio supply, and sole ammonium supply in 12d for maize (Zhengdan
 958) seedlings in hydroponic condition. Using the R (V3.3.2) XCMS package
 to identify peaks identification, peaks filtration, peaks alignment. In
 among, the main parameters are bw=5, ppm=15, peakwidth=c(10,120),
 mzwid=0.015, mzdiff=0.01, method=”centWave”. Obtain a data matrix
 including information such as“mass to charge ration, m/z”, retention time
 and intensity. In among, positive ion mode obtains 16068 precursor
 molecules and negative ion mode obtains 5259 precursor molecules for each
 N forms. The data was exported to excel for subsequent analysis. SCK, ST1
 and ST2 indicate the metabolites in the shoot of sole nitrate supply,
 mixed N supply and sole ammonium supply in 12d, respectively. RCK, RT1 and
 RT2 indicate the metabolites in the root of sole nitrate supply, mixed N
 supply and sole ammonium supply in 12d, respectively.raw-negative-positive.csvSupplementary MaterialSupplementary tables and figuresSupplementarymaterial.pdfTranscriptome raw data from maize (Zhengdan958) is uploaded to SRA database, SRA accession: PRJNA506798.Transcriptome raw data from maize (Zhengdan958) is uploaded to SRA database, SRA accession: PRJNA506798.