cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tqjq2bw3k
title: Space resource utilization of dominant species integrates abundance- and functional-based processes for better predictions of plant diversity dynamics

description: Sustainable ecosystem management relies on our ability to predict changes
 in plant diversity and to understand the underlying mechanisms. Empirical
 evidence demonstrates that abundance- and functional-based processes
 simultaneously explain the loss of plant diversity in response to human
 activities. Recently, a novel indicator based on percent cover (CoverD)
 and maximum height (HeightD) of the dominant plant species – Space
 Resource Utilization (SRUD) – has proven to give robust and better
 predictions of plant diversity dynamics than community biomass. Whether
 the superior predictive ability of SRUD is due to its capacity to
 simultaneously capture abundance- and functional-based processes remains
 unknown. Here, we tested this hypothesis by quantifying mechanistic links
 between changes in SRUD and biodiversity in response to nutrients and
 herbivores. Furthermore, we assessed the relative contribution of
 dominant, intermediate, and rare species to reduced density of individuals
 by combining null model analysis with field experiments. We found that
 SRUD successfully captured changes in ground-level light availability and
 changes in the number of individuals to predict plant diversity dynamics,
 and each of CoverD and HeightD partly and independently contributed to
 both processes. Comparative results from null model analysis and field
 experiments confirmed that individual losses of dominant, intermediate,
 and rare species followed non-random processes. Specifically, compared
 with random loss process, rare species lost proportionally more
 individuals and thus disproportionately contributed to species loss, while
 dominant and intermediate species lost less. Our results demonstrate that
 SRUD captures both abundance- and functional-based processes thus
 explaining why SRUD provides more accurate predictions of changes in
 species diversity. Given that rare species can play an important role in
 shaping community structure, resisting against invasion, impacting higher
 trophic levels, and providing multiple ecosystem functions, reducing the
 SRU of dominant species could alleviate the risk of exclusion of rare
 species by mitigating abundance- and functional-based competition
 processes.
description: Species level height, cover, biomass and abundance were obtained
 directly from field survey of quadrat. species level sru is obtained by
 multiplying the height and cover of the species. community level biomass,
 abundance and sru were obtained by adding species level biomass, abundance
 and sru, respectively.
DOI: 10.5061/dryad.w0vt4b8w1
title: Evolution along allometric lines of least resistance: Morphological differentiation in Pristurus geckos

description: Species living in distinct habitats often experience unique ecological
 selective pressures, which can drive phenotypic divergence. However, how
 ecophenotypic patterns are affected by allometric trends and trait
 integration levels is less well understood. Here we evaluate the role of
 allometry in shaping body size and body form diversity in Pristurus geckos
 utilizing differing habitats. We found that patterns of allometry and
 integration in body form were distinct in species with different habitat
 preferences, with ground-dwelling Pristurus displaying the most divergent
 allometric trend and high levels of integration. There was also strong
 concordance between intraspecific allometry across individuals and
 evolutionary allometry among species, revealing that differences in body
 form among individuals were predictive of evolutionary changes across the
 phylogeny at macroevolutionary scales. This suggested that phenotypic
 evolution occurred along allometric lines of least resistance, with
 allometric trajectories imposing a strong influence on the magnitude and
 direction of size and shape changes across the phylogeny. When viewed in
 phylomorphospace, the largest rock-dwelling species were most similar to
 the smallest ground-dwelling species, and vice versa. Thus, in Pristurus,
 phenotypic evolution along the differing habitat-based allometric
 trajectories resulted in similar body forms at differing body sizes in
 distinct ecological habitats.
description: README In this folder, you can find the code, the morphological dataset,
 and the phylogenetic data necessary for the analyses described in the
 'software' folder. # Morphological data These are the linear
 measurements in millimeters (mm) of *Pristurus* specimens
 (morpho\_pristurus.csv) and the average for each species
 (morpho\_sp\_final.csv). The linear measurements are as follows: * SVL:
 Snout-Vent Length (Body size) (mm). * TrL: Trunk Length (mm). * HL: Head
 Length (mm). * HW: Head Width (mm). * HH: Head Height (mm). * Lhu: Length
 of the humerus (mm). * Lun: Length of the ulna (mm). * Lfe: Length of the
 femur (mm). * Ltb: Length of the tibia (mm). # Phylogenetic data Consensus
 tree in Nexus format (pristurus\_tree\_final.nex) and posterior
 phylogenetic trees in RDS format (posterior\_pristurus\_final.rds) of
 *Pristurus*, extracted from a published phylogeny of Afro-Arabian
 squamates (Tejero-Cicuéndez et al. 2022 Systematic Biology).
DOI: 10.5061/dryad.k0p2ngfcd
title: Age-dependent genetic variation in aggression

description: Understanding the extent to which behavioural variance is underlain by
 genotypic, environmental and genotype-by-environment effects is important
 for predicting how behavioural traits might respond to selection and
 evolve. How behaviour varies both within and among individuals can change
 across ontogeny, leading to differences in the relative contribution of
 genetic and environmental effects to phenotypic variation across ages. We
 investigated among-individual and among-genotype variation in aggression
 across ontogeny by measuring, twice as juveniles and twice as adults, both
 approaches and attacks against a three-dimensional-printed model opponent
 in eight individuals from each of eight genotypes ( N = 64). Aggression
 was only significantly repeatable and heritable in juveniles.
 Additionally, how aggression changed between juvenile and adult
 life-history stages varied significantly among individuals and genotypes.
 These results suggest that juvenile aggression is likely to evolve more
 rapidly via natural selection than adult aggression and that the
 trajectory of behavioural change across the lifespan has the potential to
 evolve. Determining when genetic variation explains (or does not explain)
 behavioural variation can further our understanding of key life-history
 stages during which selection might drive the strongest or swiftest
 evolutionary response.
description: We collected our data by recording fish behavior and then
 counting approaches and bites toward the model. We then added approaches
 and bites to get total aggression. We used an excel document to record the
 data.  The columns in the data set include individual (a unique individual
 identification number), video (a video identifier), genotype (the genotype
 of the individual), age (the age of the fish), time (which order the video
 was taken), observer (who observed the fish), approaches (the number of
 approaches towards a model), bites (the number of bites towards a model),
 latency to move, latency to approach, latency to attack (all latencies
 were for how long it took the fish to recover from the barrier being
 removed, and approach or attack the model) graphtime (the age of the
 fish), and aggression (total number of approaches and bites). 
description: We used R studio (R version 3.4) to analyze the data. We used
 lmer from the R package lme4 to analyze our data with linear models. We
 used the rptGaussian function from the R package rptR to obtain
 heritability and repeatability.
DOI: 10.15468/dl.wcrd4d
title: Occurrence Download

description: A dataset containing 3709 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Achillea asiatica"
 ]
}

 The dataset includes 3709 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003417-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6071/m3168g
title: Expansion of wastewater-based disease surveillance to improve health equity in California’s Central Valley: Sequential shifts in case-to-wastewater and hospitalization-to-wastewater ratios

description: Introduction: Over a third of the communities (39%) in the Central Valley
 of California, a richly diverse and important agricultural region, are
 classified as disadvantaged—with inadequate access to healthcare, lower
 socio-economic status, and higher exposure to air and water pollution. The
 majority of racial and ethnic minorities are also at higher risk of
 COVID-19 infection, hospitalization, and death according to the Centers
 for Disease Control and Prevention. Healthy Central Valley Together
 established a wastewater-based disease surveillance (WDS) program that
 aims to achieve greater health equity in the region through partnership
 with Central Valley communities and the Sewer Coronavirus Alert Network.
 WDS offers a cost-effective strategy to monitor trends in SARS-CoV-2
 community infection rates. Methods: In this study, we evaluated
 correlations between public health and wastewater data (represented as
 SARS-CoV-2 target gene copies normalized by pepper mild mottle virus
 target gene copies) collected for three Central Valley communities over
 two periods of COVID-19 infection waves between October 2021 and September
 2022. Public health data included clinical case counts at county and
 sewershed scales as well as COVID-19 hospitalization and intensive care
 unit admissions. Lag-adjusted hospitalization:wastewater ratios were also
 evaluated as a retrospective metric of disease severity and corollary to
 hospitalization:case ratios. Results: Consistent with other studies,
 strong correlations were found between wastewater and public health data.
 However, a significant reduction in case:wastewater ratios was observed
 for all three communities from the first to the second wave of infections,
 decreasing from an average of 4.7 ± 1.4 over the first
 infection wave to 0.8 ± 0.4 over the second. Discussion:
 The decline in case:wastewater ratios was likely due to reduced clinical
 testing availability and test seeking behavior, highlighting how WDS can
 fill data gaps associated with under-reporting of cases. Overall, the
 hospitalization:wastewater ratios remained more stable through the two
 waves of infections, averaging 0.5 ± 0.3 and
 0.3 ± 0.4 over the first and second waves, respectively.
DOI: 10.5061/dryad.3xsj3txkz
title: Raising offspring increases ageing: Differences in senescence among three populations of a long-lived seabird, the Atlantic puffin

description: 1. Actuarial senescence, the decline of survival with age, is well
 documented in the wild. Rates of senescence vary widely between taxa, to
 some extent also between sexes, with the fastest life histories showing
 the highest rates of senescence. Few studies have investigated differences
 in senescence among populations of the same species, although such
 variation is expected from population-level differences in environmental
 conditions, leading to differences in vital rates and thus life histories.
 2. We predict that, within species, populations differing in productivity
 (suggesting different paces of life) should experience different rates of
 senescence, but with little or no sexual difference in senescence within
 populations of monogamous, monomorphic species where the sexes share
 breeding duties. 3. We compared rates of actuarial senescence among three
 contrasting populations of the Atlantic puffin Fratercula arctica. The
 data set comprised 31 years (1990–2020) of parallel capture-mark-recapture
 data from three breeding colonies, Isle of May (North Sea), Røst
 (Norwegian Sea) and Hornøya (Barents Sea), showing contrasting
 productivities (i.e. annual breeding success) and population trends. We
 used time elapsed since first capture (TFC) as a proxy for bird age, and
 productivity and the winter North Atlantic Oscillation Index (wNAO) as
 proxies for the environmental conditions experienced by the populations
 within and outside the breeding season, respectively. 4. In accordance
 with our predictions, we found that senescence rates differed among the
 study populations, with no evidence for sexual differences. There was no
 evidence for an effect of wNAO, but the population with the lowest
 productivity, Røst, showed the lowest rate of senescence. As a
 consequence, the negative effect of senescence on the population growth
 rate (λ) was up to 3–5 times smaller on Røst (Δλ = -0.009) than on the two
 other colonies. 5. Our findings suggest that environmentally induced
 differences in senescence rates among populations of a species should be
 accounted for when predicting effects of climate variation and change on
 species persistence. There is thus a need for more detailed information on
 how both actuarial and reproductive senescence influence vital rates of
 populations of the same species, calling for large-scale comparative
 studies.
DOI: 10.5061/dryad.tmpg4f52x
title: Lung proteome and metabolome endotype in HIV-associated obstructive lung disease

description: Purpose: Obstructive lung disease is increasingly common among persons
 with HIV in both smokers and non-smokers. We used aptamer proteomics to
 identify proteins and associated pathways in HIV-associated obstructive
 lung disease. Methods: Bronchoalveolar lavage fluid (BALF) samples from 26
 persons living with HIV with obstructive lung disease were matched to
 persons living with HIV without obstructive lung disease based on age,
 smoking status, and antiretroviral treatment. 6,414 proteins were measured
 using SomaScan aptamer-based assay. We used sparse distance-weighted
 discrimination (sDWD) to test for a difference in protein expression and
 permutation tests to identify univariate associations between proteins and
 forced expiratory volume in 1s precent predicted (FEV1pp). Significant
 proteins were entered into a pathway overrepresentation analysis (ORA). We
 also constructed protein-driven endotypes using K-means clustering and
 performed ORA on the proteins that were significantly different between
 clusters. We compared protein-associated clusters to those obtained from
 BALF and plasma metabolomics data on the same patient cohort. Results:
 After filtering, we retained 3872 proteins for further analysis. Based on
 sDWD, protein expression was able to separate cases and controls. We found
 575 proteins that were significantly correlated with FEV1pp after multiple
 comparisons adjustment. We identified two protein-driven endotypes, one of
 which was associated with poor lung function, and found that insulin and
 apoptosis pathways were differentially represented. We found similar
 clusters driven by metabolomics in BALF but not plasma. Conclusion:
 Protein expression differs in persons living with HIV with and without
 obstructive lung disease. We were not able to identify specific pathways
 differentially expressed among patients based on FEV1pp; however, we
 identified a unique protein endotype associated with insulin and apoptotic
 pathways.
DOI: 10.6078/d1671x
title: A highly contiguous genome assembly for the California quail (Callipepla californica)

description: The California quail (Callipepla californica) is an iconic native bird of
 scrub and oak woodlands in California and the Baja Peninsula of Mexico.
 Here, we report a draft reference assembly for the species generated from
 PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as
 part of the California Conservation Genomics Project (CCGP). Sequenced
 reads were assembled into 321 scaffolds totaling 1.08 Gb in length.
 Assembly metrics indicate a highly contiguous and complete assembly with a
 contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness
 score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome,
 more than previous Odontophoridae quail assemblies but in line with
 estimates of TE content for recent long-read assemblies of chicken and
 Peking duck. Together these metrics indicate that the present assembly is
 more complete than prior reference assemblies generated for Odontophoridae
 quail. This reference will serve as an essential resource for studies on
 local adaptation, phylogeography, and conservation genetics in this
 species of significant biological and recreational interest.
description: We performed <em>de
 novo </em>repeat annotation of the draft California quail reference
 assembly using the program RepeatModeler2 with the ltrstruct option
 selected to improve identification of LTR elements (Flynn et al. 2020).
 The resulting repeat library contained 496 elements and was used to
 annotate transposable element diversity in the California quail assembly
 using RepeatMasker (Smit et al. 2015).
DOI: 10.5061/dryad.3n5tb2rmr
title: Data for: Inundation depth stimulates plant-mediated CH4 emissions by increasing ecosystem carbon uptake and plant height in an estuarine wetland

description: Plant-mediated CH4 emission is an important part of the ecosystem CH4
 emission from vegetated wetlands. Inundation depth may alter the potential
 magnitude of CH4 releases by changing CH4 production and
 plant transport, but the relationships between plant-mediated
 CH4 emissions and inundation depth are still uncertain,
 especially for estuarine wetlands with changeable hydrological processes.
 Besides, there are conflicting results regarding the role of inundation
 depth in plant-mediated CH4 emissions. Here we conducted a novel
 inundation depth experiment (0, 5, 10, 20, 30 and 40 cm inundation depth)
 dominated by Phragmites australis in the Yellow River estuary, China. Soil
 CH4 emissions, ecosystem CH4 emissions, net ecosystem
 CO2 exchange (NEE), soil organic carbon (SOC) and plant traits were
 measured during the growing seasons of 2018, 2019 and 2020. Plant-mediated
 CH4 emissions were the difference between ecosystem
 CH4 emissions and soil CH4 emissions. The results showed
 that inundation depth decreased soil CH4 emissions but increased
 ecosystem CH4 emissions. Plant-mediated CH4 transport
 from Phragmites australis accounted for 99% of total ecosystem
 CH4 emissions under different inundation depths. Inundation depth
 strongly stimulated plant-mediated CH4 emission from 0 to 20 cm
 during the growing seasons. The increased net ecosystem CO2 exchange
 enhanced plant-mediated CH4 emissions by altering production,
 suggesting that carbon components derived from photosynthetic carbon input
 may benefit CH4 production. Additionally, the increased plant
 height promoted CH4 emission by regulating plant transport,
 indicating that plant traits may play an important role in transport of
 CH4. Our findings indicated that NEE and plant height play an important
 role in plant-mediated CH4 emissions under different inundation
 depths in estuarine wetland. This study also highlights that hydrological
 regimes and plant traits are essential for the estimation of
 CH4 emissions in future projections of global wetland changes.
DOI: 10.5061/dryad.b2rbnzskh
title: Herbivory selects for tolerance and constitutive defence across stages of community succession

description: Plants defend themselves from herbivory by either reducing damage
 (resistance) or minimizing its negative fitness effects with compensatory
 growth (tolerance). Factors mediating the selection for defenses such as
 herbivory and competition are in constant flux in an early secondary
 successional community, which can create temporal variation in selection
 for these traits. We manipulated successional age of the community and
 insect herbivory in a genotypic selection experiment with the perennial
 herb Solidago altissima. We found selection for investment in aboveground
 biomass in early succession but not in mid-succession, suggesting that the
 importance of competition is highest in the very first years of
 succession. Herbivory selected for smaller and better defended plants in
 both successional ages but decreased plant survival and probability of
 flowering only in mid-succession. Despite dramatic differences in
 herbivory between early and mid-succession, selection on defense traits
 did not change. These results demonstrate that changes in the community
 that affect key life-history traits in an individual species can occur
 over very short timescales in a dynamic secondary successional
 environment. Such temporal variation may be an important, yet overlooked,
 contributor to adaptive mosaics across populations.
DOI: 10.5517/ccdc.csd.cc2clml6
title: CCDC 2192648: Experimental Crystal Structure Determination

description: Related Article: Jiawei Lin|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n72ss
title: CCDC 2449675: Experimental Crystal Structure Determination

description: Related Article: ruonan Yao|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.