cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9cnp5hqjf
title: Phylogenomic and macroevolutionary evidence for an explosive radiation of a plant genus in the Miocene

description: Mountain systems harbor a substantial fraction of global biodiversity and,
 thus, provide excellent opportunities to study rapid diversification and
 to understand the historical processes underlying the assembly of
 biodiversity hotspots. The rich biodiversity in mountains is widely
 regarded as having arisen under the influence of geological and climatic
 processes as well as the complex interactions among them. However, the
 relative contribution of geology and climate in driving species radiation
 is seldom explored. Here, we studied the evolutionary radiation of
 Oreocharis (Gesneriaceae), which has diversified extensively throughout
 East Asia, especially within the Hengduan Mountains (HDM), using
 transcriptomic data and a time calibrated phylogeny for 88% (111/126) of
 all species of the genus. In particular, we applied phylogenetic
 reconstructions to evaluate the extent of incomplete lineage sorting
 accompanying the early and rapid radiation in the genus. We then fit
 macroevolutionary models to explore its spatial and diversification
 dynamics in Oreocharis and applied explicit birth-death models to
 investigate the effects of past environmental changes on its
 diversification. Evidence from 574 orthologous loci suggest that
 Oreocharis underwent an impressive early burst of speciation starting ca.
 12 Ma in the Miocene, followed by a drastic decline in speciation toward
 the present. Although we found no evidence for a shift in diversification
 rate across the phylogeny of Oreocharis, we showed a difference in
 diversification dynamics between the HDM and non-HDM lineages, with higher
 diversification rates in the HDM. The diversification dynamic of
 Oreocharis is most likely positively associated with temperature-dependent
 speciation and dependency on the Asian monsoons. We suggest that the warm
 and humid climate of the mid-Miocene was probably the primary driver of
 the rapid diversification in Oreocharis, while mountain building of the
 HDM might have indirectly affected species diversification of the HDM
 lineage. This study highlights the importance of past climatic changes,
 combined with mountain building, in creating strong environmental
 heterogeneity and driving diversification of mountain plants, and suggests
 that the biodiversity in the HDM cannot directly be attributed to mountain
 uplift, contrary to many recent speculations.
description: <strong>DATA & FILE
 OVERVIEW</strong>
 <strong>data:</strong><br>
 <strong>CenozoicTemperature from 65 Ma</strong><br>
 CenozoicTemperature.txt <strong>Asian Monsoons
 from 15 Ma</strong><br> AsianMonsoonsfrom_15 Ma.txt
 <strong>File List:</strong>
 <strong>Appendices S1-S17</strong>
DOI: 10.5061/dryad.3ffbg79j4
title: Dispersal patterns in black howler monkeys (Alouatta pigra): Integrating multi-year demographic and molecular data

description: Dispersal is a fundamental process in the functioning of animal societies
 as it regulates the degree to which closely related individuals are
 spatially concentrated. A species’ dispersal pattern can be complex as it
 emerges from individuals’ decisions shaped by the cost-benefit tradeoffs
 associated with either remaining in the natal group or dispersing. Given
 the potential complexity, combining long-term demographic information with
 molecular data can provide important insights into dispersal patterns of a
 species. Based on a 15-year study that integrates multi-year demographic
 data on six groups with longitudinal and cross-sectional genetic sampling
 of 20 groups (N=169 individuals, N=21 polymorphic microsatellite loci), we
 describe the various dispersal strategies of male and female black howler
 monkeys (Alouatta pigra) inhabiting Palenque National Park, Mexico.
 Genetically confirmed dispersal events (N=21 of 59 males; N=6 of 65
 females), together with spatial autocorrelation analyses revealed that the
 dispersal pattern of black howlers is bisexual with strong sex-biases in
 both dispersal rate (males disperse more often than females) and dispersal
 distance (females disperse farther than males). Observational and genetic
 data confirm that both males and females can successfully immigrate into
 established groups, as well as form new groups with other dispersing
 individuals. Additionally, both males and females may disperse singly, as
 well as in pairs, and both may also disperse secondarily. Overall, our
 findings suggest multiple dispersal trajectories for black howler males
 and females, and longer multi-year studies are needed to unravel which
 demographic, ecological, and social factors underlie individuals’
 decisions about whether to disperse and which dispersal options to take.
description: Data include genotype data of 181 black howler monkeys residing
 in 20 social groups inhabiting Palenque National Park, Mexico. Between
 2006 and 2020, fecal samples were collected when we could identify the
 defecator and when samples were uncontaminated by other fecal material.
 Fresh fecal material (~1 g) was placed in a 7 ml vial with 1.5 ml of
 RNAlater and subsequently stored at -18 °C until transportation to the
 Molecular Anthropology Laboratory at New York University for samples
 collected in 2006–2007 and to the Primate Molecular Ecology and Evolution
 Laboratory at the University of Texas at Austin for samples collected
 since 2010. Each individual was genotyped for up to 21 polymorphic
 microsatellite markers. We repeated homozygous genotype calls at least
 four times and heterozygous genotype calls at least two times.
 The data also include the geographic coordinates (in UTM within
 the 15 Q zone) of the 18 groups sampled in 2012. These data were used in
 the spatial autocorrelation analyses. 
description: See supplementary material associated with the publication for
 additional information on demography.
DOI: 10.5061/dryad.05qfttf36
title: In situ polyaniline coating of Prussian blue as cathode material for sodium-ion battery

description: Prussian blue has great potential for using as a sodium cathode material
 owing to its high working potential and cube frame structure. Herein, this
 work reports a two-step method to synthesize Prussian blue with ascorbic
 acid (AA) as the ball-milling additive, which improves electrochemical
 rate performance of Prussian blue during the traditional co-precipitation
 method. The obtained Prussian blue sample exhibited a superior specific
 capability (113.3 mAh g-1 even at 20 C, 1 C=170 mA g-1) and a specific
 capacity retention of 84.8% after 100 cycles at 1 C rate. In order to
 enhance the cycling performance of the Prussian blue, an in situ
 polyaniline (PANI) coating strategy was employed in which aniline was
 added into the electrolyte and polymerized under electrochemical
 conditions. The coated anode exhibited a high specific capacity retention
 of 62.7% after 500 cycles, which is significantly higher than that of the
 non-coated sample which only remains 40.1% after 500 cycles. This
 development has shown a great potential as a low-cost, high-performance
 and environmental-friendly technology for large-scale industrial
 application of PB.
DOI: 10.5061/dryad.7pvmcvdsv
title: Genome-wide SNP analysis of male and female rice field frogs, Hoplobatrachus rugulosus, supports a non-genetic sex determination system

description: Sex determination systems (SDSs) in anurans are diverse and have undergone
 independent evolutionary transitions among species. The mode of sexual
 reproduction of the rice field frog (Hoplobatrachus rugulosus), an
 economically viable edible amphibian species, is not well known. Previous
 studies have proposed that threshold temperature conditions may determine
 sex in these frogs. To elucidate the SDS in H. rugulosus, we karyotyped 10
 male and 12 female frogs, and performed fluorescence in situ hybridization
 combined with sequencing analyses using DArTseq™. Our results revealed a
 highly conserved karyotype with no sex chromosome heteromorphism, and the
 sequencing analyses did not identify any consistent sex-linked loci,
 supporting the hypothesis of temperature-dependent sex determination. The
 results of this study, and others, on SDSs in the rice field frog and
 related species also provides support for the theory that heteromorphic
 sex chromosomes may lead to an evolutionary trap that prevents variable
 SDSs. These findings add important information to the body of knowledge on
 H. rugulosus and are likely to have a significant impact on the
 productivity and economic success of rice field frog farming.
DOI: 10.5061/dryad.1vhhmgqt3
title: Continuous forest inventory of Swanton Pacific Ranch

description: C.F.I. plots are part of long term forest monitoring program on the lands
 of Cal Poly's Swanton Pacific Ranch that monitor forest conditions
 over time. Approximately two hundred, 1/5 acre fixed plots are spaced out
 in a systematic random sampling system over forested areas that results in
 a 2-3% sample size. Plot measurement began in 1997 and re-measurement
 occurs every 10 years. Information taken at each of these plots consists
 of: plot number, slope, aspect, declination, date, crew, number in crew,
 plot notes, regeneration tally, tree and snag inventory, species, witness
 trees, distance and bearing to each tree in the plot, diameter at breast
 height (DBH) to a .10 inches, height, crown class, height to crown base
 (HTCB), damage and disease, breast height age, radial growth, plot photos,
 plot comments, Herbaceous Vegetative Groundcover (consists of species
 identification and % occupation), student use difficulty, and Poison Oak
 Level (P.O. level).
DOI: 10.5061/dryad.6hdr7sr1c
title: Fitness benefit plays a vital role in the retention of the Pi-ta susceptible alleles

description: In plants, large numbers of R genes, which segregate as loci with
 alternative alleles conferring different resistance to pathogens, have
 been maintained over a long evolutionary time. In theory, there seem to be
 no reason for hosts to harbor susceptible alleles in view of their null
 contribution to resistance. As such, why should populations support
 disease-susceptible individuals along with disease-resistant individuals?
 In rice, a single copy gene Pi-at segregates for two expressed clades of
 alleles, one resistant and the other susceptible. We simulated
 loss-of-function of the Pi-ta susceptible allele using the CRISPR/Cas9
 system to detect subsequent fitness changes and obtained insights into
 fitness effects on retention of the Pi-ta susceptible allele. Our creation
 of artificial knockout of the Pi-ta susceptible allele suffered a fitness
 decline of up to 49% in term of filled grains yield upon the loss of
 Pi-ta's function. The Pi-ta susceptible alleles might serve as an
 off-switch to the downstream immune signaling, thus contributing to
 fine-tuning of plant defense response. These findings highlight the
 interplay between genetic architecture and fitness effects of segregating
 R gene alleles and also provide a plausible explanation how host genomes
 can tolerate the possible genetic load associated with a vast repertoire
 of R genes. This attempt to evaluate the fitness effect of the R gene in
 crop will bring some clues to researchers and breeders that not all
 disease resistant genes will bring fitness cost as universally
 acknowledged.
DOI: 10.5061/dryad.dfn2z3524
title: Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet

description: Conservation strategies centred around species habitat protection rely on
 species’ dietary information. One species at the focal point of
 conservation efforts is the herbivorous grouse, the western capercaillie
 (Tetrao urogallus), which is an indicator species for forest biodiversity
 conservation. Non-molecular means used to study their diet are
 time-consuming and at low taxonomic resolution. This delays the
 implementation of conservation strategies including resource protection
 due to uncertainty about its diet. Thus, limited knowledge on diet is
 hampering conservation efforts. Here we use non-invasive environmental DNA
 (eDNA) metabarcoding on DNA extracted from faeces to present the first
 large-scale molecular dietary analysis of capercaillies. Faecal samples
 were collected from seven populations located in Norway (Finnmark, Troms,
 Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We
 detected 122 plant taxa belonging to 46 plant families of which 37.7% of
 the detected taxa could be identified at species level. The average
 dietary richness of each sample was 7 ± 5 SD taxa. The most frequently
 occurring plant groups with the highest relative read abundance (RRA) were
 trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus,
 respectively. There was a difference in dietary composition (RRA) between
 samples collected from the different locations (adonis pseudo F5,86=
 11.01, r2 = 0.17, p = 0.001) and seasons (adonis pseudo F2,03 = 0.64, r2 =
 0.01, p = 0.036). Dietary composition also differed between sexes at each
 location (adonis pseudo F1,47 = 2.77, r2 = 0.04, p = 0.024), although not
 significant for all data combined. In total, 35 taxa (36.8% of taxa
 recorded) were new capercaillie food items compared to existing knowledge
 from non-molecular means. The non-invasive molecular dietary analysis
 applied in this study provides new ecological information of
 capercaillies’ diet, improving our understanding of adequate habitat
 required for their conservation.
DOI: 10.15468/dl.5ty82j
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Aerial surveys of cetaceans in the Zeehan, Apollo and Beagle Australian Marine Parks, Australia (2021-2024)"
 ]
}

 The dataset includes 104 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002875-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rxwdbrv8q
title: Spatial targeting of Screening + Eave tubes (SET), a house-based malaria control intervention, in Côte d’Ivoire: A geostatistical modelling study

description: New malaria control tools and tailoring interventions to local contexts
 are needed to reduce the malaria burden and meet global goals. The housing
 modification, screening plus a targeted house-based insecticide delivery
 system called the In2Care® Eave Tubes, has been shown to reduce clinical
 malaria in a large cluster randomised controlled trial. However, the
 widescale suitability of this approach is unknown. We aimed to predict
 household suitability and define the most appropriate locations for
 ground-truthing where Screening + Eave Tubes (SET) could be implemented
 across Côte d’Ivoire. We classified DHS sampled households into suitable
 for SET based on the walls and roof materials. We fitted a Bayesian
 beta-binomial logistic model using the integrated nested Laplace
 approximation (INLA) to predict suitability of SET and to define priority
 locations for ground-truthing and to calculate the potential population
 coverage and costs. Based on currently available data on house type and
 malaria infection rate, 31% of the total population and 17.5% of the
 population in areas of high malaria transmission live in areas suitable
 for SET. The estimated cost of implementing SET in suitable high malaria
 transmission areas would be $46m ($13m –$108m). Ground-truthing and more
 studies should be conducted to evaluate the efficacy and feasibility of
 SET in these settings. The study provides an example of implementing
 strategies to reflect local socio-economic and epidemiological factors,
 and move beyond blanket, one-size-fits-all strategies.
DOI: 10.5061/dryad.sbcc2fr6q
title: Extended data for: Screening for antifolate and artemisinin resistance in Plasmodium falciparum clinical isolates from three hospitals of Eritrea

description: Background: Antimalarial drug resistance is a major challenge hampering
 malaria control and elimination. Plasmodium falciparum, the leading
 causative parasite species, has developed resistance to basically all
 antimalarials. Continued surveillance of drug resistance using genetic
 markers provides important molecular data for treatment policies. This
 study sought to verify the genetic mechanism of resistance to
 sulfadoxine-pyrimethamine and assess the occurrence of point mutations
 associated with artemisinin resistance in P. falciparum clinical isolates
 from Eritrea. Methods: Nineteen dried blood spot samples were collected
 from patients visiting Adi Quala, Keren and Gash Barka Hospitals, Eritrea.
 The patients were followed up after receiving treatment with first line
 artesunate-amodiaquine. Nested polymerase chain reaction and Sanger
 sequencing techniques were employed to genotype point mutations in the P.
 falciparum bifunctional dihydrofolate reductase-thymidylate synthase
 (Pfdhfr, PF3D7_0417200), dihydropteorate synthase (Pfdhps, PF3D7_0810800)
 and kelch 13 (PfK13, PF3D7_1343700) genes. Results: Eight of nineteen
 (42%) of the dried blood spot samples were successful for
 PCR-amplification. Data analyses of the PCR-positive isolates revealed the
 following point mutations: Pfdhfr N51I in four isolates, C59R in one
 isolate, S108N in four isolates, a rare non-synonymous substitution V45A
 in four isolates and Pfdhps K540E in four isolates. No PfK13 point
 mutations were reported. Conclusions: Pfdhfr C59R and Pfdhps K540E point
 mutations are reliable markers for the sulfadoxine-pyrimethamine quintuple
 mutant haplotype combination. These findings highlight first reports in
 Eritrea, which verify the underlying genetic mechanism of antifolate
 resistance. Continuous monitoring of the PfK13 marker is recommended.
DOI: 10.5061/dryad.nzs7h44rw
title: Improving intra- and inter-annual GPP predictions by using individual-tree inventories and leaf growth dynamics

description: Carbon sequestration is a key ecosystem service provided by forests.
 Inventory data based on individual trees are considered to be the most
 accurate method for estimating forest productivity. However, estimations
 of forest photosynthesis itself from inventory data remains understudied,
 particularly when considering the growth and development of individual
 trees under the background of global change. Here, we used the leaf growth
 process with phenology and non-structural carbohydrates (NSC) storage to
 revise an individual-tree based carbon model, FORCCHN. This model couples
 leaf development and biomass to quantify gross primary productivity (GPP)
 in the forests, where growth is decoupled from photosynthesis in daily
 step. The model was initialized with inventory-based forest data rather
 than the more widely used satellite-based data. We tested the model
 against measured aboveground woody biomass, growth of leaf biomass, daily
 gross ecosystem exchange (GEE), and yearly GEE at five representative
 forest sites in the Northern Hemisphere. We also compared the results from
 the original model and the revised model at five forest sites. Including
 leaf growth dynamics and inventory-based initialization improved the
 predicted performance (r2) of GPP by an average of 33%. Synthesis and
 applications. Our results suggest that the appropriate vegetation data
 sources (i.e. inventory or satellite selection) and the effective
 predictions of the growth process should be considered when developing
 future carbon cycle models and forest carbon estimation options. Applying
 and improving such carbon models to evaluate carbon sequestration is an
 important part of forest carbon sink management.
description: The predicted GPP data are provided by the FORCCHN2 model. The
 data include five representative sites (i.e. Blodgett Forest, California,
 USA (Blodgett); Changbai Mountain, Jilin, China (Changbai); Harvard
 Forest, Massachusetts, USA (Harvard); Pasoh Forest Reserve, Negeri
 Sembilan, Malaysia (Pasoh); and University of Michigan Biological Station,
 Michigan, USA (Michigan)). These five forests comprise four different
 forest types: deciduous broadleaf forest (DBF), evergreen needle-leaf
 forest (ENF), evergreen broadleaf forest (EBF), and mixed forest (MF). The
 data include the results simulated by leaf area and the results simulated
 by inventory.
description: The file name is the site number. The readme file contains
 a description of each site in the dataset.
DOI: 10.5061/dryad.f1vhhmgx7
title: Changes in plant species richness due to land use and nitrogen deposition across the globe

description: Data and scripts corresponding to the article "Combined
 effects of land use and nitrogen deposition on plant species richness
 worldwide". In the article, we quantified the combined
 effects of land use and nitrogen deposition on terrestrial plant species
 richness at a 0.25º spatial resolution across the globe. We first
 determined the proportional changes in plant species richness for
 different land-use types and N deposition values through meta-analyses of
 local monitoring data obtained from the literature. We then combined the
 site-level responses with global land use and N deposition maps in a new
 multi-pressure species-area relationship (mp-SAR) model to provide
 estimates of changes in plant species richness at a resolution of 0.25º
 (about 25 km at the equator) worldwide. In this repository you will find
 all the data necessary to get the final results and the code in R to guide
 you through out the analysis.
description: We quantified the combined effects of land use and nitrogen
 deposition on terrestrial plant species richness at a 0.25º spatial
 resolution across the globe. We first determined the proportional changes
 in plant species richness for different land-use types and N deposition
 values through meta-analyses of local monitoring data obtained from the
 literature. We then combined the site-level responses with global land use
 and N deposition maps in a new multi-pressure species-area relationship
 (mp-SAR) model to provide estimates of changes in plant species richness
 at a resolution of 0.25º (about 25 km at the equator) worldwide.
description: All the scripts are commented out so they should be easy to
 follow. R environment and version: <br> platform
       x86_64-w64-mingw32          <br> arch           x86_64        
              <br> os             mingw32                  
   <br> system         x86_64, mingw32             <br> status
                                     <br> major          4          
                 <br> minor          0.2                      
   <br> year           2020                        <br> month  
        06                          <br> day            22          
                <br> svn rev        78730                    
   <br> language       R                           <br>
 version.string R version 4.0.2 (2020-06-22)<br> nickname      
 Taking Off Again