cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sj3tx9677
title: COVID-19 epidemic in Fiji

description: This study involves the estimation of a key epidemiological parameter for
 evaluating and monitoring the transmissibility of a disease. The
 time-varying reproduction number is the index for quantifying the
 transmissibility of infectious diseases. Accurate and timely estimation of
 the time-varying reproduction number is essential for optimising
 non-pharmacological interventions and movement control orders during
 epidemics. The time-varying reproduction number for the second wave of the
 pandemic in Fiji is estimated using the popular EpiEstim R package and the
 publicly available COVID-19 data from 19 April 2021 to 01 December 2021.
 Our findings show that the non-pharmacological interventions and movement
 control orders introduced and enforced by the Fijian Government had a
 significant impact in preventing the spread of COVID-19. Moreover, the
 results show that many restrictions were either relaxed or eased when the
 time-varying reproduction number was below the threshold value of 1. The
 results have equipped some information on the second wave of the COVID-19
 pandemic that could be used in the future as a guide for public health
 policymakers in Fiji. Estimation of time-varying reproduction numbers
 would be helpful for continuous monitoring of the effectiveness of the
 current public health policies that are being implemented in Fiji.
description: The publicly available data for the daily new confirmed COVID-19
 cases was obtained from the official website of Fiji’s Ministry of Health
 and Medical Services
 (MOHFiji)(https://www.health.gov.fj/covid-19-updates/)
DOI: 10.5061/dryad.7pvmcvdwb
title: Adult breeding monarch relative abundance

description: Many insects are in clear decline, with monarch butterflies (Danaus
 plexippus) drawing particular attention as a flagship species. It is well
 documented that, among migratory populations, numbers of overwintering
 monarchs have been falling across several decades, but trends among
 breeding monarchs are less clear. Here, we compile &gt; 135,000
 monarch observations between 1993-2018 from the North American Butterfly
 Association’s annual butterfly count to examine spatiotemporal patterns
 and potential drivers of adult monarch relative abundance trends across
 the entire breeding range in eastern and western North America. While the
 data revealed declines at some sites, particularly the US Northeast and
 parts of the Midwest, numbers in other areas, notably the US Southeast and
 Northwest, were unchanged or increasing, yielding a slightly positive
 overall trend across the species range. Negative impacts of agricultural
 glyphosate use appeared to be counterbalanced by positive effects of
 annual temperature, particularly in the US Midwest. Overall, our results
 suggest that population growth in summer is compensating for losses during
 the winter and that changing environmental variables have offsetting
 effects on mortality and/or reproduction. We suggest that
 density-dependent reproductive compensation when lower numbers arrive each
 spring is currently able to maintain relatively stable breeding monarch
 numbers. However, we caution against complacency since accelerating
 climate change may bring growing threats. Our data also suggest that
 increases of summer monarchs in some regions, especially in the west and
 far south, may reflect replacement of migratory with resident populations.
 Nonetheless, it is perhaps reassuring that ubiquitous downward trends in
 summer monarch abundance are not evident.
DOI: 10.5061/dryad.gf1vhhmsf
title: Data from: Simulated evolution of mating signal diversification in a primate radiation

description: Divergence in allopatry and subsequent diversification of mating signals
 on secondary contact (reinforcement) is a major driver of phenotypic
 diversity. Observing this evolutionary process directly is often
 impossible, but simulated evolution can pinpoint key drivers of phenotypic
 variation. We developed evolutionary simulations in which mating signals,
 modelled as points in phenotype space, evolve across time under varying
 evolutionary scenarios. We model mate recognition signals in guenons, a
 primate radiation exhibiting colourful and diverse face patterns
 hypothesized to maintain reproductive isolation via mate choice. We
 simulate face pattern evolution across periods of allopatry and sympatry,
 identifying the role of key parameters in driving evolutionary endpoints.
 Results show that diversification in allopatry and assortative mate choice
 on secondary contact can induce rapid phenotypic diversification,
 resulting in distinctive (between species) and stereotyped (within
 species) face patterns, similar to extant guenons. Strong selection
 against hybrids is key to diversification, with even low levels of hybrid
 fitness often resulting in merged populations on secondary contact. Our
 results support a key role for reinforcement by assortative mating in the
 maintenance of species diversity and support the
 long-proposed prehistorical scenario for how such striking
 diversity was produced and maintained in perhaps the most colourful of all
 mammalian clades.
DOI: 10.5061/dryad.34tmpg4nj
title: Generation of hybrids in broadly sympatric ducks

description: Although rare, hybrids are more common in broadly sympatric waterfowl than
 in any other avian family; yet, the behavioral ecology explaining their
 generation has remained controversial. Leading hypotheses are forced
 interspecific copulations, mis-imprinting caused by mixed broods, and
 scarcity of conspecific mates. Using a large sample of hybrid ducks
 solicited from North American hunters we evaluated these hypotheses by
 genetically determining the mother and father species of F1 hybrids. Based
 on abundances in areas where their breeding ranges overlap, the frequency
 of hybrids varied greatly from expectations, with hybrids between species
 within recently derived clades being much more frequent than those between
 more divergent clades. Forced copulations, as measured by large phallus
 length asymmetries between parentals, strongly predicted the father
 species of most F1 hybrids. Thus, most Anas acuta x A. platyrhynchos
 (Northern Pintail x Mallard) F1s were sired by A. acuta, and most A.
 platyrhynchos x Mareca strepera (Mallard x Gadwall) F1s were sired by A.
 platyrhynchos. Siring asymmetries were consistent with phallus length
 asymmetries in five additional parental combinations, but none had samples
 large enough to be individually statistically significant. The exception
 to this trend was our sample of nine A. platyrhynchos x Mareca americana
 (Mallard x Gadwall) F1s, for which a large phallus asymmetry failed to
 predict the father species. Hybrids were rare in brood parasitic species,
 suggesting mis-imprinting to be an unlikely cause of most hybrids;
 however, our samples of hybrids from regular brood parasites were
 inadequate to strongly address this hypothesis. We could test the scarcity
 of mates hypothesis for only a single hybrid combination and it
 contradicted our prediction: most F1 M. Penelope x M. americana (Eurasian
 x American Wigeon) were sired by M. penelope, strongly contradicting our
 prediction that female M. penelope wintering in enormous flocks of M.
 americana (American Wigeon) on the west coast of North America would have
 difficulty finding conspecific mates. In general, our results support
 interspecific forced copulations as the predominant behavioral mechanism
 generating hybrids in North temperate waterfowl.
description: ddRAD sequencing and Sanger sequencing of mtDNA genes.
DOI: 10.5061/dryad.c2fqz61bn
title: Original data of diatom communities in two alpine lakes of eastern China

description: This study explored ecological responses of Erye and Sanye lakes to
 climate change and atmospheric deposition based on multi-proxy sedimentary
 records in the Taibai Mountain (eastern China). Diatom communities of the
 two study lakes shifted from large-sized benthic taxa to small fragilariod
 species after the mid-20th century, synchronous with an increase in diatom
 production and a decrease in mean length of diatom valves. Changes in
 diatom communities were significantly correlated with nitrogen deposition
 in both lakes and climate warming in the upstream lake. 
description: Diatom samples were treated
 using 10% HCl and 30% H<sub>2</sub>O<sub>2</sub>
 according to standard procedures. Taxonomy was mainly based on Krammer and
 Lange‐Bertalot (1986-1991)
 using an Olympus BX53 microscope with an oil immersion objective at 1000. A
 minimum of 300 valves were
 counted in each sample. Diatom concentrations were calculated by counting
 a known area on a pipetted strewn slide, made from a 0.5 mL aliquot from a
 13 mL ‘well-mixed’ suspension of ~ 0.5 - 1 g dry sediments. Meanwhile,
 length of each identified valve was measured using cellSens software
 installed in the Olympus microscope.
DOI: 10.5061/dryad.h44j0zpnw
title: Hotspots within a hotspot: Evolutionary measures unveil interesting biogeogeographic patterns for the conservation of the coastal forest in Chile

description: Aim: Given the continuous loss of biodiversity, there is an
 urgent need to study its patterns to generate conservation measures.
 Complementing the traditional patterns with indices that incorporate
 evolutionary aspects such as phylogenetic diversity or phylogenetic
 endemism (PD and PE) allows us to infer possible historical processes that
 could explain the conformation of current biodiversity. Coastal forests in
 Chile are part of a biodiversity hotspot of high endemism that is under
 threat. In this study, patterns of richness and endemism were determined
 and contrasted with the evolutionary indices PD, PE, PDres (residual PD),
 RPD (relative PD), and RPE (relative PE) to infer historical processes
 that could have shaped the current diversity patterns. We also compared
 these indices at different taxonomic levels. Location: Thirteen sites on a
 latitudinal gradient between 30°S and 40°S that are part of the Chilean
 Coastal mountain range. Taxon: Woody flora at the species level.
 Methods: DNA was extracted and three genes were sequenced for 95%
 of the species. A phylogeny was constructed to calculate evolutionary
 indices based on PD and PE and compared at different taxonomic
 levels.  Results: The results of PD and PE were
 spatially consistent with those of richness and endemism, but
 evolutionarily important sites were discovered. PD-derived indices
 indicate three evolutionary hotspots, a cradle-type site with a
 predominance of neoendemisms (generating recent diversity) at 33°S, two
 museum-type sites with a predominance of paleoendemisms (maintaining
 relict diversity) at 30°S and 40°S and the last one with high PD and PE at
 37°. Main conclusion: We found interesting evolutionary hotspots
 within the hotspot of Central Chile with different characteristics.
 Incorporating measures that consider the evolutionary aspect has important
 implications for the conservation of highly diverse and endemic areas.
description: This is a concatenated data matrix obtained from GenBank and
 laboratory work, that was used to perform phylogenetic analyses.
DOI: 10.5061/dryad.4j0zpc8f2
title: Model outputs from NYC-VPRM and STILT

description: Modeled biogenic CO2 fluxes from the NYC-VPRM (the Vegetation
 Photosynthesis and Respiration Model for New York City) and modeled
 atmospheric CO2 concentration enhancements by STILT (the Lagrangian
 Atmospheric Transport model). The model outputs are used for findings
 presented in the manuscript titled "High resolution modeling of
 vegetation reveals large summertime biogenic CO2 fluxes in New York
 City" by Dandan Wei, Andrew Reinmann, Luke Schiferl, and Roisin
 Commane and published in Environmental Research Letters.
DOI: 10.15468/dl.ynya4s
title: Occurrence Download

description: A dataset containing 2941 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parthenos sylvia"
 ]
}

 The dataset includes 2941 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003136-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.95x69p8nm
title: Stable-isotopes (δ2H, δ13C) within feathers from harvested American black ducks (2017-2020)

description: Stable isotope data from American Black Duck feathers (n = 665) and
 associated harvest data. The first primary feather (P1) was collected from
 wings submitted to the Species Composition Survey in Canada and Parts
 Collection Survey in the United States. From available feathers, we
 selected individuals for stable-isotope analysis stratified by black duck
 conservation region, sex, age, and date of harvest, where possible. These
 data are those that were selected for stable-hydrogen isotope analysis.
 See Kusack et al. (in press) - 'Origins of harvested American black
 ducks: stable isotopes support the flyover hypothesis' for additional
 information on our use of this data.
description: The first primary feather (P1) was collected from wings submitted
 to the Species Composition Survey in Canada and Parts Collection Survey in
 the United States. All individuals were assigned a species identity, age,
 and sex, if possible, by trained waterfowl biologists. They were also
 assigned a date and location of harvest as provided by the hunter.
 Individuals were assigned to a region of harvest based on (a) the provided
 latitude and longitude of harvest (or the listed province when missing
 latitude and longitude) for feathers obtained from the Species Composition
 Survey, and (b) county of harvest, for feathers obtained from the Parts
 Collection Survey. In the few cases (n = 43) where the county spanned two
 conservation regions, we assigned the individual to the conservation
 region within which the county centroid fell. Feathers were processed for
 δ2H and δ13C at the University of Western Ontario’s Laboratory for Stable
 Isotope Science Advanced Facility for Avian Research (LSIS-AFAR)
 laboratory (London, ON, Canada) and the Cornell Lab of Ornithology Isotope
 Lab (COIL; Ithaca, NY, USA). All feathers were processed for δ2H. All
 feathers from adults were processed for δ13C, but only a subset of samples
 from juveniles (n = 90 randomly selected) was processed for
 δ13C.
DOI: 10.57745/4lzq7l
title: Preterm human breast milk nutriome microbiome exposome infant growth

description: Background: Prematurity increases the risk of neonatal mortality and long-term health issues, such as obesity and cardiovascular disease. Breastfeeding benefits preterm infants by reducing necrotizing enterocolitis, improving cognition, and supporting early growth, although the mechanisms underlying these benefits are unclear. Objective: Within the exposome-framework, the combined influence of breast milk nutritional, microbiological, and toxicological components on preterm infant growth during hospitalization was explored. Methods: In the single-center prospective observational LACTACOL cohort (NCT01493063), weight and body composition were assessed on 137 exclusively breastfed preterm infants (28-34 weeks), with discharge-weight and fat-free mass (FFM) Z-scores as growth indicators. An omic-scale characterization of breast milk's nutritional, microbiological, and toxicological composition combined with an exploratory multivariate random forest analysis helped identify predictive components of both growth indicators. Results: Combined endogenous and exogenous breast milk compartments predicted discharge weight and FFM Z-scores with 34% and 42% accuracy, respectively, driven by the nutriome (24%). Key regulators of weight gain included choline-containing lipid species enriched in lauric, linoleic, and/or oleic acids and under sphingolipid and phosphatidylcholine forms; as well as carnitine and glucogenic amino acids. Exposome (contribution 19%) and microbiome (12%) components, such as dioxin-like, polychlorinated biphenyls, and bacteria (Enterobacter, Corynebacterium), were strong predictors of FFM, alongside bioactive lipids as sphingolipids and phospholipids enriched in nervonic and oleic acids, or eicosapentanoic acid and its oxylipin. Conclusions: These findings deepen our understanding of breast milk components’ benefits for preterm infant early growth and emphasize the potential importance of bioactive lipids, in promoting infant healthy growth and long-term outcomes. The data of nutriome-exposome-micorbiome of preterm milk are synthetized in this dataset English (2025-03-20).
DOI: 10.6086/d13d51
title: Data For: Soil NH3 emissions across an aridity, soil pH, and N deposition gradient in southern California

description: Soil ammonia (NH3) emissions are often overlooked pathways for ecosystem N
 loss; however, they may help sustain ecosystem nitrogen (N) limitation,
 especially in arid regions where hydrologic N losses are relatively small.
 To characterize controls over NH3 emissions, we measured NH3 losses from
 six dryland sites along a gradient in soil pH, atmospheric N deposition,
 and rainfall. We also added ammonium (NH4+) to determine whether emissions
 were limited by N. Soil NH3 emissions were positively correlated with pH
 (R2 = 0.90, p = 0.002), reaching 24.2 ± 16.0 µg N-NH3 m-2 hr-1 at the most
 alkaline site. Wetting soils with NH4+ solutions increased NH3 emissions
 from alkaline and moderately acidic soils (F1,35 = 14.7, p &lt;
 0.001), suggesting that N can stimulate NH3 volatilization regardless of
 pH. These results suggest that both pH and N act as proximate controls
 over NH3 losses and that these losses can reduce soil N accumulation.
description: Please see methods in the associated manuscript.
description: These data represent soil ammoina emission from six dryland sites
 in Southern California. Empty cells indicate that data are missing for a
 given observation.
DOI: 10.7272/q69s1p9g
title: Proteome-wide antigenic profiling in Ugandan cohorts identifies associations between age, exposure intensity, and responses to repeat-containing antigens in Plasmodium falciparum

description: Protection against Plasmodium falciparum, which is primarily
 antibody-mediated, requires recurrent exposure to develop. The study of
 both naturally acquired limited immunity and vaccine induced protection
 against malaria remains critical for ongoing eradication efforts. Towards
 this goal, we deployed a customized P.
 falciparum PhIP-seq T7 phage display library
 containing 238,068 tiled 62-amino acid peptides,
 covering all known coding regions, including antigenic variants, to
 systematically profile antibody targets in 198 Ugandan children and adults
 from high and moderate transmission settings. Repeat elements –
 short amino acid sequences repeated within a protein – were significantly
 enriched in antibody targets. While breadth of responses to
 repeat-containing peptides was twofold higher in children living
 in the high versus moderate exposure setting, no such differences were
 observed for peptides without repeats, suggesting that antibody
 responses to repeat-containing regions may be more exposure dependent
 and/or less durable in children than responses to regions without
 repeats. Additionally, short motifs associated with
 seroreactivity were extensively shared among hundreds of antigens,
 potentially representing cross-reactive epitopes. PfEMP1 shared
 motifs with the greatest number of other antigens, partly driven
 by the diversity of PfEMP1 sequences. These data suggest that the large
 number of repeat elements and potential cross-reactive epitopes found
 within antigenic regions of P.
 falciparum could contribute to the inefficient nature of
 malaria immunity.
DOI: 10.5061/dryad.h9w0vt4mb
title: Elevated O3 inhibited isoprene emission of a diploid and a triploid genotype of Populus tomentosa by different mechanisms

description: Ozone (O3) pollution affects plant growth and
 isoprene (ISO) emission. However, the
 response mechanism of isoprene emission rate (ISOrate)
 to elevated O3 (EO3) remains poorly understood. ISOrate was investigated
 in two genotypes (diploid and triploid) of Chinese white poplar
 (Populus tomentosa Carr.) exposed to EO3 in an open top
 chamber (OTC) system. The triploid genotype had higher
 photosynthesis rate (A) and stomatal conductance (gs) than the
 diploid one. EO3 significantly decreased A, gs, and
 ISOrate of middle and lower leaf positions in both genotypes.
 In the diploid genotype, the reduction of ISOrate was caused by
 a systematic decrease related to ISO synthesis capacity,
 as indicated by decreased contents of isoprene precursor
 dimethylallyl diphosphate (DMADP) and isoprene synthase
 (ISPS) protein and activity of ISPS. On the other hand,
 the negative effect of O3 on ISOrate of the
 triploid genotype did not result from
 inhibited ISO synthesis capacity, but from increased ISO
 oxidative loss within the leaf. Our findings will be useful for breeding
 poplar genotypes with high-yield and lower ISOrate, depending on
 local atmospheric VOC/NOx ratio, to cope with both the rising
 O3 concentrations and increasing biomass demand. They
 can also enlighten the incorporation of O3 effects into
 process-based models of isoprene emission.
description: The study was carried out in an experimental station at Yanqing
 (40°47′N, 116°34′E), northwest of Beijing, China. Data from two seedlings
 per genotype per OTC were averaged, and single OTC was treated as the
 statistical unit.
DOI: 10.5061/dryad.9w0vt4bj3
title: Data for: Dark matters – contrasting responses of stream biofilm to browning and loss of riparian shading

description: Concentrations of terrestrial-derived dissolved organic carbon (DOC) in
 freshwater ecosystems have increased consistently, causing freshwater
 browning. The mechanisms behind browning are complex, but in
 forestry-intensive regions browning is accelerated by land drainage.
 Forestry actions in streamside riparian forests alter canopy shading,
 which together with browning is expected to exert a complex and largely
 unpredictable control over key ecosystem functions. We conducted a stream
 mesocosm experiment with three levels of browning (ambient vs. moderate
 vs. high, with 2.7 and 5.5-fold increase, respectively, in absorbance)
 crossed with two levels of riparian shading (70% light reduction vs. open
 canopy) to explore the individual and combined effects of browning and
 loss of shading on the quantity (algal biomass) and nutritional quality
 (polyunsaturated fatty acid and sterol content) of the periphytic biofilm.
 We also conducted a field survey of differently colored (4.7 to 26.2 mg
 DOC L-1) streams to provide a ‘reality check’ for our experimental
 findings. Browning reduced greatly the algal biomass, suppressed the
 availability of essential polyunsaturated fatty acids, especially
 eicosapentaenoic acid (EPA), and sterols, but increased the availability
 of terrestrial-derived long-chain saturated fatty acids (LSAFA). In
 contrast, loss of shading increased primary productivity, which resulted
 in elevated sterol and EPA content of the biofilm. The field survey
 largely repeated the same pattern: biofilm nutritional quality decreased
 significantly with increasing DOC, as indicated particularly by a decrease
 of the w-3:w-6 ratio and increase in LSAFA content. Algal
 biomass, in contrast, was mainly controlled by dissolved inorganic
 nitrogen (DIN) concentration, while DOC concentration was of minor
 importance. The ongoing browning process is inducing a dramatic reduction
 in the nutritional quality of the stream biofilm. Such degradation of the
 major high-quality food source available for stream consumers may reduce
 the trophic transfer efficiency in stream ecosystems, potentially
 extending across the stream-forest ecotone.
description: See the article (Dark matters – contrasting responses of stream
 biofilm to browning and loss of riparian shading) for details of data
 collection and processing.
description: The data can be viewed and edited using Microsoft Excel or
 alternative spreadsheet software.