cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sbcc2fr8r
title: Genome-structural analyses support an allotetraploid origin of the walnut family from within Myricaceae and shared genome duplications reveal substitution rate variation

description: In lineages of allopolyploid origin, entire parental subgenomes may
 coexist, with two or more sets of homoeologous chromosomes that differ in
 gene content and syntenic structure. Presence or absence of genes, and
 microsynteny along chromosomal blocks, can be used to differentiate
 subgenomes and can be coded as phylogenetic data. We assembled
 chromosome-level genomes of representative species across an ancient
 allopolyploid lineage, the walnut family (Juglandaceae), with Myrica and
 other Fagales as outgroups, and used genome-structural data to infer a
 phylogeny. Microsynteny (with various collinear block sizes) and gene
 content analyses, using the dominant or recessive progenitor subgenomes or
 both, all yielded identical topologies that place Engelhardia (a SE Asian
 and Central American clade) with Platycarya, an enigmatic monospecific
 taxon endemic in East Asia, but well-represented in the Paleocene-Eocene
 of North America and Europe. Morphological studies including fossils also
 found the Platycarya/Engelhardia clade because of leaf architecture,
 floral morphology, and nut walls without lacunae, but DNA-alignment-based
 phylogenetics carried out here and in previous studies never detected this
 uniformly wind-dispersed clade, instead grouping Platycarya with Carya and
 Juglans. The novel analyses further reveal the family’s hybrid origin from
 extinct or unsampled progenitors nested within Myricaceae and that
 Rhoiptelea chiliantha, the Chinese sister species to all other
 Juglandaceae, contains proportionally more genes related to DNA repair and
 evolved at a rate 2.6- to 3.5-times slower than the remaining species. Our
 results have implications for the molecular clock hypothesis and suggest
 that genomic structure contains so-far undervalued phylogenetic signal.
description: This dataset is about the input genome data for microsynteny- and
 gene-content-based approaches, which infer parental lineages and subgenome
 relationships in the family.
DOI: 10.5061/dryad.pc866t1rj
title: Code: A model of wild bee populations accounting for spatial heterogeneity and climate induced temporal variability of food resources at the landscape level

description: The viability of wild bee populations and the pollination services that
 they provide are driven by the availability of food resources during their
 activity period and within the surroundings of their nesting sites.
 Changes in climate and land use influence the availability of these
 resources and are major threats to declining bee populations. Because wild
 bees may be vulnerable to interactions between these threats, spatially
 explicit models of population dynamics that capture how bee populations
 jointly respond to land use at a landscape scale and weather are needed.
 Here, we developed a spatially and temporally explicit theoretical model
 of wild bee populations aiming for a middle ground between the existing
 mapping of visitation rates using foraging equations and more refined
 agent-based modelling. The model is developed for Bombus sp. and captures
 within-season colony dynamics. The model describes mechanistically
 foraging at the colony level and temporal population dynamics for an
 average colony at the landscape level. Stages in population dynamics are
 temperature-dependent triggered with a theoretical generalized seasonal
 progression, which can be informed by growing degree days (GDD). The
 purpose of the LandscapePhenoBee model is to evaluate the impact of
 systematic changes and within-season variability in resources on bee
 population sizes and crop visitation rates. In a simulation study, we used
 the model to evaluate the impact of the shortage of food resources in the
 landscape arising from extreme drought events in different types of
 landscapes (ranging from different proportions of semi-natural habitats
 and early and late flowering crops) on bumblebee populations.
description: This dataset contains all the code to be able to simulate the
 data used in the manuscript.
DOI: 10.5061/dryad.rbnzs7hdd
title: Unraveling the effects of cold stratiﬁcation and temperature on the seed germination of invasive Spartina alterniﬂora across latitude

description: Seed germination is critical to the life history of plants, playing an
 important role in the successful recruitment, colonization, and even
 invasion of new individuals within and outside population distribution
 ranges. Cold stratiﬁcation and temperature are the key factors affecting
 seed germination traits. Studying how these two factors drive geographical
 variation in seed germination is essential to analyze and predict the
 geographical distribution range of alien plants in novel habitats.
 Spartina alterniﬂora, native to the United States, was introduced into
 China in 1979 and has spread over 20° of latitude along the eastern coast
 of China. Germination plays a crucial role in S. alterniﬂora’s large-scale
 invasion and diffusion across latitude. To evaluate the effects of cold
 stratiﬁcation and temperature on seed germination of S. alterniﬂora across
 latitude, we collected seeds at seven locations across latitude in China.
 We exposed these provenances to cold stratiﬁcation at 4°C (0, 1, 3, and 5
 months) and germination temperature (5°C, 15°C, 25°C, and 35°C) treatments
 in growth chambers. Seed germination was observed for 98 days, and we
 calculated germination rate, germination index, and germination time.
 Results indicated that longer cold stratiﬁcation signiﬁcantly promoted
 germination rate and germination index, but decreased germination time.
 Similarly, higher germination temperature signiﬁcantly promoted
 germination rate and germination index, but decreased germination time.
 Moreover, there were signiﬁcant interactive effects on germination traits
 between cold stratiﬁcation and temperature. Seed germination traits showed
 linear relationships with latitude, indicating that S. alterniﬂora seeds
 from different provenances germinated at different times and adopted
 different germination strategies. The stratiﬁcation and temperature are
 the most important factors regulating the dormancy and germination seeds,
 so they can be important drivers of this variation along latitude. Under
 scenarios of warmer regional temperature, seeds at higher latitudes could
 germinate earlier and higher germination rate, which would favor a
 potential northern expansion of this invasive plant.
description: We collected <em>Spartina alterniflora</em> seeds at
 seven locations across latitude in China. We exposed these provenances to
 cold stratiﬁcation at 4°C (0, 1, 3, and 5 months) and germination
 temperature (5°C, 15°C, 25°C, and 35°C) treatments in growth chambers.
 Seed germination was observed for 98 days, and we calculated germination
 rate, germination index, and germination time.
DOI: 10.5061/dryad.mcvdnck36
title: Cryptic species in a colorful genus: integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species

description: Several cryptic avian species have been validated by recent
 integrative taxonomic efforts in the Sino-Himalayan mountains, indicating
 that avian diversity in this global biodiversity hotspot may be
 underestimated. In the present study,we investigated species limits in the
 genus Tarsiger, the bush robins, a group of montane forest
 specialists with high species richness in the Sino-Himalayan region. Based
 on comprehensive sampling of all 11 subspecies of the six currently
 recognized species, we applied an integrative taxonomic approach by
 combining multilocus, acoustic, plumage and morphometric analyses. Our
 results reveal that the isolated north-central Chinese populations
 of Tarsiger cyanurus, described as the
 subspecies albocoeruleus but usually considered invalid,
 is distinctive in genetics and vocalisation, but only marginally
 differentiated in morphology. We also found the Taiwan endemic T.
 indicus formosanus to be distinctive in genetics, song and
 morphology from T. i. indicus and T.
 i. yunnanensis of the Sino-Himalayan mountains.
 Moreover, Bayesian species delimitation using BPP suggests that
 both albocoeruleus and formosanus merit full species status. We propose their treatment as ‘Qilian Bluetail’ T. albocoeruleus and ‘Taiwan Bush Robin’ T. formosanus, respectively.
description: NA=Missing value in Supplementary files
DOI: 10.5281/zenodo.18400575
title: LLM_Facility_Analysis
DOI: 10.5281/zenodo.18400576
title: LLM_Facility_Analysis
DOI: 10.5061/dryad.j9kd51cfx
title: Human thymidylate synthase ITC data

description: This dataset includes isothermal titration calorimetry measurements of
 human thymidylate synthase (hTS) binding its product deoxythymidine
 monophosphate (TMP) and an N-terminal trunction of hTS binding its
 substrate deoxyuridine monophosphate (dUMP). These measurements include
 heats produced at various enzyme and ligand concentrations. Analysis of
 these data provide binding free energies, enthalpies, and entropies for
 these binding events. We find that in contrast to hTS binding its
 substrate dUMP, which we have previously shown to have positive
 cooperativity, hTS binding TMP and the N-terminally truncated hTS binding
 dUMP are non-cooperative. Details of the data collection and analysis can
 be found in the associated publication.
DOI: 10.5061/dryad.n2z34tmzz
title: Local earthquake coda waveform from the Jammu And Kashmir Seismological NETwork (JAKSNET)

description: This dataset contains local earthquake coda waveform and pre-signal noise
 waveforms from the Jammu And Kashmir Seismological NETwork (JAKSNET), a
 joint endeavor between the Indian Institute of Science Education and
 Research Kolkata (IISER-K), Shri Mata Vaishno Devi University (SMVD) and
 the University of Cambridge, UK. The network was initiated in July 2013
 and comprised 24 broadband seismograph systems deployed across the
 J&K Himalaya. A total of 696 vertical component coda waveforms,
 from 121 small-to-moderate local earthquakes of magnitude between 3.0 and
 5.5, within the epicentral distance of 200 km are provided in this
 database. Pre-signal representative noise from 22 stations, which recorded
 these earthquakes, have been provided for computing signal-to-noise ratio
 for the coda signal. The waveform data is sampled at 100 samples per
 second (sps),  are corrected for instrument response, and
 filtered in the frequency band of 0.02 to 30 Hz. Coda waveforms start from
 twice the S-wave arrival time and are of 90 s duration. This data has been
 used to compute the seismic coda-wave attenuation of the Jammu and Kashmir
 Himalaya. The manuscript is submitted for review in JGR Solid Earth and
 this dataset complements the manuscript. 
description: The data was recorded by the JAKSNET experiment between 2013 and
 2018. The waveform data is sampled at 100 samples per second (sps), are
 corrected for instrument response and filtered in the frequency band of
 0.02 to 30 Hz. Coda waveforms start from twice the S-wave arrival time and
 are of 90 s duration. The representative noise is of 10 s duration before
 the P-wave arrival of the earthquake.
DOI: 10.5061/dryad.gf1vhhmsc
title: Rhesus macaque cone ratio heritability

description: A defining feature of catarrhine primates is uniform trichromacy – the
 ability to distinguish red (long; L), green (medium; M), and blue (short;
 S) wavelengths of light. While the tuning of photoreceptors is conserved,
 the ratio of L:M cones in the retina is variable within and between
 species, with human cone ratios differing from other catarrhines. Yet, the
 sources and structure of variation in cone ratios are poorly understood,
 precluding a broader understanding of color vision variability. Here, we
 report a large-scale study of a pedigreed population of macaques. We
 collected foveal RNA and analysed opsin gene expression using cDNA. We
 estimated the additive genetic variance of cone ratios. The average L:M
 ratio and standard error was 1.03:1± 0.02. There was no age effect, and
 genetic contribution to variation was negligible. We found marginal sex
 effects with females having larger ratios than males. S cone ratios
 (0.143: 1± 0.002) had significant genetic variance with a heritability
 estimate of 43% but did not differ between sexes or age groups. Our
 results contextualize the derived human condition of L-cone dominance and
 provide new information about the heritability of cone ratios and
 variation in primate color vision.
description: Cone ratio expression was determined through the use of droplet
 digital PCR, which is an absolute gene expression method. This provided
 the phenotypic information for color vision effects. 
 Pedigree information was acquired from the Caribbean Primate
 Research Center, which has been managing the population of the Cayo
 Santiago Rhesus macaques. The pedigree confirms sex, age, and parental
 information of all macaques involved in the study. All
 analyses were done with R and R studio using the following packages:
 tidyverse (Wickham et al.
 2019), reshape2 (Wickham
 2020), lans2r (Polerecky et al.
 2012), lubridate (Grolemund and
 Wickham 2011) and ggplot2 (Wilkinson
 2011).
description: Pedigree information and individual identifiers of the monkeys in
 the study have been changed to anonymous names. All data were analyzed in
 R, and the code provided is set up for R script running.
DOI: 10.5061/dryad.prr4xgxph
title: Database PCA: A middle Pleistocene Homo from Nesher Ramla, Israel

description: It has long been believed that Neanderthals originated and flourished on
 the European continent. However, recent morphological and genetic studies
 have suggested that they may have received a genetic contribution from a
 yet unknown non-European group. Here we report on the recent discovery of
 archaic Homo fossils from the site of Nesher Ramla, Israel, which we dated
 to 140,000 to 120,000 years ago. Comprehensive qualitative and
 quantitative analyses of the parietal bones, mandible, and lower second
 molar revealed that this Homo group presents a distinctive combination of
 Neanderthal and archaic features. We suggest that these specimens
 represent the late survivors of a Levantine Middle Pleistocene paleodeme
 that was most likely involved in the evolution of the Middle Pleistocene
 Homo in Europe and East Asia.
DOI: 10.5281/zenodo.18400561
title: LINF_320012300

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18400562
title: LINF_320012300

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.kprr4xh6r
title: Data for: Protective geometry and reproductive anatomy as candidate determinants of clutch size variation in pentatomid bugs

description: Many animals lay their eggs in clusters. Eggs on the periphery of clusters
 can be at higher risk of mortality. We asked whether the most commonly
 occurring clutch sizes in pentatomid bugs could result from geometrical
 arrangements that maximize the proportion of eggs in the cluster’s
 interior. Although the most common clutch sizes do not correspond with
 geometric optimality, stink bugs do tend to lay clusters of eggs in shapes
 that protect increasing proportions of their offspring as clutch sizes
 increase. We also considered whether ovariole number, an aspect of
 reproductive anatomy that may be a fixed trait across many pentatomids,
 could explain observed distributions of clutch sizes. The most common
 clutch sizes across many species correspond with multiples of ovariole
 number. However, there are species with the same number of ovarioles that
 lay clutches of widely varying size, among which multiples of ovariole
 number are not over-represented. In pentatomid bugs, reproductive anatomy
 appears to be more important than egg mass geometry in determining clutch
 size uniformity. In addition, within this group of animals that has lost
 most of its variation in ovariole number, clutches with a broad range of
 shapes and sizes may still be laid. 
description: Part of the dataset was collected from different research
 laboratories studying stink bugs (Hemiptera: Pentatomidae) that recorded
 clutch sizes laid by their bugs in the course of their research. The other
 dataset was collected from analysis of photographs of stink bug eggs from
 online sources and photographs taken by study co-authors. The R code
 provided on Zenodo ( https://doi.org/10.5281/zenodo.6557606 ) makes use of the .csv files to generate figures and analyses for this paper, which is in press at the American Naturalist currently.
description: R code required to process the data is available here: https://doi.org/10.5281/zenodo.6557606
DOI: 10.5061/dryad.0zpc8670w
title: Data from: Estimating survival and adoption rates of dependent juveniles

description: 1. Population growth and fitness are typically most sensitive to adult
 survival in long-lived species, but variation in recruitment often
 explains most of the variation in fitness, as past selection has canalized
 adult survival. Estimating juvenile survival until age of independence has
 proven challenging, because marking individuals in this age class may
 directly affect survival. For Greater Sage-grouse, uniquely marking
 juveniles in the first days of life likely results in adverse effects to
 survival, detection of juveniles is not perfect, and females adopt
 juveniles from other parents. These challenges are encountered by
 researchers studying avian and mammalian species with similar life
 histories, yet, methods do not exist that explicitly estimate all these
 components of the recruitment process. 2. We propose a novel data
 collection method and demographic model to simultaneously estimate rates
 of detection, survival, and adoption of juvenile individuals. Using
 multiple cameras to film the beginning of juvenile activity on specific
 days, we obtained counts of juveniles associated with marked females.
 Increases of juveniles to broods provided information that enabled us to
 estimate rates of adoption that can be applied at the population level.
 Losses from broods informed apparent survival. These losses could be
 attributed to death, or they could be chicks that were adopted by other
 females. 3. We found evidence that apparent survival of juveniles was
 influenced by localized weather patterns when chicks were young.
 Similarly, we found that young chicks were more susceptible to the adverse
 effect of attending females being flushed by an observer. Both of these
 patterns diminished quickly as chicks aged. We provide the first-ever
 estimates of interval-specific adoption rates. 4. Our results suggest that
 researchers should be cautious when designing studies to estimate juvenile
 survival. More importantly, they provide insight into adoption, a behavior
 that has been known to exist for decades.
DOI: 10.15468/dl.2d3gjs
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichopsis paraguariensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 83 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003129-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h18931zp7
title: Behavioural and morphological traits influence sex-specific floral resource use by hummingbirds

description: Research on resource partitioning in plant-pollinator mutualistic systems
 is mainly concentrated at the levels of species and communities, whereas
 differences between males and females are typically ignored. Nevertheless,
 pollinators often show large sexual differences in behaviour and
 morphology, which may lead to sex-specific patterns of resource use with
 the potential to differentially affect plant reproduction and
 diversification. We investigated variation in behavioural and
 morphological traits between sexes of hummingbird species as potential
 mechanisms underlying sex-specific flower resource use in ecological
 communities. To do so, we compiled a dataset of plant-hummingbird
 interactions based on pollen loads for 31 hummingbird species from 13
 localities across the Americas, complemented by data on territorial
 behaviour (territorial or nonterritorial) and morphological traits (bill
 length, bill curvature, wing length and body mass). We assessed the extent
 of intersexual differences in niche breadth and niche overlap in floral
 resource use across hummingbird species. Then, we tested whether floral
 niche breadth and overlap between sexes are associated with sexual
 dimorphism in behavioural or morphological traits of hummingbird species,
 while accounting for evolutionary relatedness among the species. We found
 striking differences in patterns of floral resource use between sex.
 Females had a broader floral niche breadth and were more dissimilar in the
 plant species visited with respect to males of the same species, resulting
 in a high level of resource partitioning between sexes. We found that both
 territoriality and morphological traits were related to sex-specific
 resource use by hummingbird species. Notably, niche overlap between sexes
 was greater for territorial than nonterritorial species, and moreover,
 niche overlap was negatively associated with sexual dimorphism in bill
 curvature across hummingbird species. These results reveal the importance
 of behavioural and morphological traits of hummingbird species in
 sex-specific resource use and that resource partitioning by sex is likely
 to be an important mechanism to reduce intersexual competition in
 hummingbirds. These findings highlight the need for better understanding
 the putative role of intersexual variation in shaping patterns of
 interactions and plant reproduction in ecological communities.
DOI: 10.57903/uj/pgqtuf
title: Raw proteomic analysis data of murine aorta: an effect of aging and humanised dyslipidaemia

description: Raw proteomic analysis data (.raw) of aorta obtained from 8-week-old and 40-week-old humanised dyslipidaemic male and female mice as compared to age and sex-matched wild type mice
DOI: 10.5061/dryad.7sqv9s4v9
title: Plant size-dependent influence of foliar fungal pathogens promotes diversity through allometric growth

description: The data was collected in the northeastern Qinghai-Tibetan Plateau,
 Qinghai Province, China (101° 18′ 57″ E, 37° 36′ 50″ N; 3 221 m a.s.l.) in
 2019 and 2020, including the species-specific growth allometry (scaling
 exponent and intercept) fitted by the allometric equation under each
 treatment in a population-level experiment, i.e., control, fungicide
 application, neighbor removal (removal), fungicide application × neighbor
 removal, and the community-level mean and dispersion of the growth
 allometry (CWM and FDis of growth scaling exponent and intercept,
 respectively) weighted by the species cover for each plot in a
 community-level fungicide application experiment.
description: # Plant size-dependent influence of foliar fungal pathogens promotes
 diversity through allometric growth
 The data was collected in
 the northeastern Qinghai-Tibetan Plateau, Qinghai Province, China (101°
 18′ 57″ E, 37° 36′ 50″ N; 3 221 m a.s.l.) in 2019 and 2020, including the
 species-specific growth allometry (scaling exponent and intercept) fitted
 by the allometric equation under each treatment in a population-level
 experiment, i.e., control, fungicide application, neighbor removal
 (removal), fungicide application × neighbor removal, and the
 community-level mean and dispersion of the growth allometry (CWM and FDis
 of growth scaling exponent and intercept, respectively) weighted by the
 species cover for each plot in a community-level fungicide
 application experiment.