cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hm2047nh
title: Data from: Hybrid swarm between divergent lineages of mule deer (Odocoileus hemionus)

description: Studies of hybrid zones have revealed an array of evolutionary outcomes,
 yet the underlying structure is typically characterized as one of three
 types: a hybrid zone, a hybrid swarm or a hybrid taxon. Our primary
 objective was to determine which of these three structures best
 characterizes a zone of hybridization between two divergent lineages of
 mule deer (Odocoileus hemionus), mule deer and black-tailed deer. These
 lineages are morphologically, ecologically and genetically distinct, yet
 hybridize readily along a zone of secondary contact between the east and
 west slopes of the Cascade Mountains (Washington and Oregon, USA). Using
 microsatellite and mitochondrial DNA, we found clear evidence for
 extensive hybridization and introgression between lineages, with varying
 degrees of admixture across the zone of contact. The pattern of
 hybridization in this region closely resembles a hybrid swarm; based on
 data from 10 microsatellite loci, we detected hybrids that extend well
 beyond the F1 generation, did not detect linkage disequilibrium at the
 centre of the zone and found that genotypes were associated randomly
 within the zone of contact. Introgression was characterized as
 bidirectional and symmetric, which is surprising given that the zone of
 contact occurs along a sharp ecotone and that lineages are characterized
 by large differences in body size (a key component of mating success).
 Regardless of the underlying mechanisms promoting hybrid swarm
 maintenance, it is clear that the persistence of a hybrid swarm presents
 unique challenges for management in this region.
description: Deer hybrid swarm
 dataSample ID, geographic
 location (latitude and longitude) and genotypes at 10 microsatellite loci
 for 410 individual mule deer and black-tailed deer collected in Oregon and
 Washington, USA. Zeros indicate missing genotypes.
DOI: 10.5281/zenodo.18238281
title: Datasets of Four-hourly Temperature, Relative Humidity, and Wet Bulb Temperature during Hot-Wet Extremes in Summer over the Beijing-Tianjin-Hebei Region

description: This dataset contains meteorological observation data from the Beijing-Tianjin-Hebei (BTH) region of China, with a focus on heat and humidity indicators. The data structure is as follows:Temporal resolution: four times a day (Beijing Time 02:00, 08:00, 14:00, 20:00).1. Figure_1c_national_bth_wetbulb_temperature_1991_2020.txt: Regional mean wet-bulb temperature of BTH (1991-2020) based on an anonymized station network. Unit: °C.2. National_BTH_station_data.nc: Data from 176 national meteorological stations (coordinates obfuscated).3. AWSs_urban_region_mean.txt: Summer (May to September) regional mean values for urban areas (temperature, relative humidity, wet-bulb temperature) from 2009 to 2024. Daily records run from 08:00 to 02:00 (LST) of the next day.4. AWSs_rural_region_mean.txt: Summer (May to September) regional mean values for rural areas (same variables) from 2009 to 2024, following the same daily time convention.
DOI: 10.5061/dryad.59j4m
title: Data from: Body size variation in aquatic consumers causes pervasive community effects, independent of mean body size

description: Intraspecific phenotypic variation is a significant component of
 biodiversity. Body size, for example, is variable and critical for
 structuring communities. We need to understand how homogenous and
 variably-sized populations differ in their ecological responses or effects
 if we are to have a robust understanding of communities. We manipulated
 body size variation in consumer (tadpole) populations in mesocosms (both
 with and without predators), keeping mean size and density of these
 consumers constant. Size-variable consumer populations exhibited stronger
 antipredator responses (reduced activity), which had a cascading effect of
 increasing the biomass of the consumer’s resources. Predators foraged less
 when consumers were variable in size, and this may have mediated the
 differential effects of predators on the community composition of
 alternative prey (zooplankton). All trophic levels responded to
 differences in consumer size variation, demonstrating that intrapopulation
 phenotypic variability can significantly alter interspecific ecological
 interactions. Furthermore, we identify a key mechanism (size thresholds
 for predation risk) that may mediate impacts of size variation in natural
 communities. Together, our results suggest that phenotypic variability
 plays a significant role in structuring ecological communities.
description: carlson langkilde ecol
 evol 2017Complete dataset for
 tadpoles, newts, and zooplankton. Data are separated into separate
 worksheets, with additional worksheets defining variable
 names.
DOI: 10.5281/zenodo.18238280
title: Datasets of Four-hourly Temperature, Relative Humidity, and Wet Bulb Temperature during Hot-Wet Extremes in Summer over the Beijing-Tianjin-Hebei Region

description: This dataset contains meteorological observation data from the Beijing-Tianjin-Hebei (BTH) region of China, with a focus on heat and humidity indicators. The data structure is as follows:Temporal resolution: four times a day (Beijing Time 02:00, 08:00, 14:00, 20:00).1. Figure_1c_national_bth_wetbulb_temperature_1991_2020.txt: Regional mean wet-bulb temperature of BTH (1991-2020) based on an anonymized station network. Unit: °C.2. National_BTH_station_data.nc: Data from 176 national meteorological stations (coordinates obfuscated).3. AWSs_urban_region_mean.txt: Summer (May to September) regional mean values for urban areas (temperature, relative humidity, wet-bulb temperature) from 2009 to 2024. Daily records run from 08:00 to 02:00 (LST) of the next day.4. AWSs_rural_region_mean.txt: Summer (May to September) regional mean values for rural areas (same variables) from 2009 to 2024, following the same daily time convention.
DOI: 10.5061/dryad.q1r19
title: Data from: Live imaging of symbiosis: spatiotemporal infection dynamics of GFP-labelled Burkholderia symbiont in the bean bug Riptortus pedestris

description: Many insects possess endosymbiotic bacteria inside their body, wherein
 intimate interactions occur between the partners. While recent
 technological advancements have deepened our understanding of metabolic
 and evolutionary features of the symbiont genomes, molecular mechanisms
 underpinning the intimate interactions remain difficult to approach
 because the insect symbionts are generally uncultivable. The bean bug
 Riptortus pedestris is associated with the betaproteobacterial
 Burkholderia symbiont in a posterior region of the midgut, which develops
 numerous crypts harbouring the symbiont extracellularly. Distinct from
 other insect symbiotic systems, R. pedestris acquires the Burkholderia
 symbiont not by vertical transmission but from the environment every
 generation. By making use of the cultivability and the genetic
 tractability of the symbiont, we constructed a transgenic Burkholderia
 strain labelled with green fluorescent protein (GFP), which enabled
 detailed observation of spatiotemporal dynamics and the colonization
 process of the symbiont in freshly prepared specimens. The symbiont live
 imaging revealed that, at the second instar, colonization of the symbiotic
 midgut M4 region started around 6 h after inoculation (hai). By 24 hai,
 the symbiont cells appeared in the main tract and also in several crypts
 of the M4. By 48 hai, most of the crypts were colonized by the symbiont
 cells. By 72 hai, all the crypts were filled up with the symbiont cells
 and the symbiont localization pattern continued during the subsequent
 nymphal development. Quantitative PCR of the symbiont confirmed the
 infection dynamics quantitatively. These results highlight the
 stinkbug-Burkholderia gut symbiosis as an unprecedented model for
 comprehensive understanding of molecular mechanisms underpinning insect
 symbiosis.
description: Data (Kikuchi
 Yoshitomo)Fitness parameters of
 symbiont infected (Bu+) and uninfected (Bu-) insects. Sheets: survival
 rate, male's fitness parameters, female's fitness parameters,
 time to reproduction, egg numbers, and symbiont titer.
DOI: 10.5061/dryad.4gg73
title: Data from: Functional significance of petals as landing sites in fungus-gnat pollinated flowers of Mitella pauciflora (Saxifragaceae)

description: Despite the well-known visual attraction function of angiosperm petals,
 additional roles of these floral organs (e.g. the provision of
 landing-site platforms for pollinators) have rarely been examined. This is
 likely because most petals perform multiple functions, making it difficult
 to isolate the importance of landing sites in pollination success. We
 investigated the landing-site function of dull-coloured pinnately branched
 petals in Mitella pauciflora flowers, which are predominantly pollinated
 by fungus gnats. We conducted a field experiment, in which the effects of
 experimental petal removal on pollinators’ approach, landing and visit
 duration and floral reproductive success were examined in naturally
 pollinated flowers. According to direct and time-lapse camera
 observations, petal removal did not influence pollinators’ approach
 frequency or visit duration, but did significantly decrease their
 landings. Fruit set and pollen dispatch both significantly decreased with
 petal removal, indicating that petals promote female and male reproductive
 success in M. pauciflora by facilitating pollinator landing. This
 demonstrates that inconspicuous petals primarily have a landing-site
 function rather than a visual attraction function in M. pauciflora.
 Discriminating between diverse petal functions is a challenging problem,
 and new approaches are required to elucidate the functional features of
 angiosperm flowers.
description: Katsuhara_et_al_data_for_FuncEcolAll data archived here were used for GLMM analyses in Katsuhara et al. "Functional significance of petals as landing site in fungus-gnats pollinated flowers of <i>Mitella pauciflora</i> (Saxifragaceae). Data is in six worksheets.
DOI: 10.5061/dryad.50q65s0
title: Data from: Stabilizing selection, mutational bias and the evolution of sex

description: Stabilizing selection around a fixed phenotypic optimum is expected to
 disfavor sexual reproduction, since asexually reproducing organisms can
 maintain a higher fitness at equilibrium, while sex disrupts combinations
 of compensatory mutations. This conclusion rests on the assumption that
 mutational effects on phenotypic traits are unbiased, that is, mutation
 does not tend to push phenotypes in any particular direction. In this
 paper, we consider a model of stabilizing selection acting on an arbitrary
 number of polygenic traits coded by bialellic loci, and show that
 mutational bias may greatly reduce the mean fitness of asexual populations
 compared with sexual ones in regimes where mutations have weak to moderate
 fitness effects. Indeed, mutation and drift tend to push the population
 mean phenotype away from the optimum, this effect being enhanced by the
 low effective population size of asexual populations. In a second part, we
 present results from individual-based simulations showing that positive
 rates of sex are favored when mutational bias is present, while the
 population evolves towards complete asexuality in the absence of bias. We
 also present analytical (QLE) approximations for the selective forces
 acting on sex in terms of the effect of sex on the mean and variance in
 fitness among offspring.
description: C++ simulation
 programProgram simulating a
 haploid, facultatively sexual population undergoing stabilizing selection
 on an arbitrary number of quantitative phenotypic traits, and with genetic
 variation for the rate of sex.program.tar
DOI: 10.6084/m9.figshare.31154556
title: Rovibrational computations for He2+X2Σu+ including non-adiabatic, relativistic and QED corrections

description: We report the potential energy curve, the diagonal Born-Oppenheimer, non-adiabatic mass, relativistic, and leading-order quantum-electrodynamical (QED) corrections for the ground electronic state of the helium dimer cation; the higher-order QED and finite-nuclear size effects are also estimated. The computations are carried out with an improved error control and over a broader configuration range compared to earlier work [D. Ferenc, V. I. Korobov, and E. Mátyus, Phys. Rev. Lett. 125, 213001 (2020)]. As a result, all rovibrational bound states are reported with an estimated accuracy of 0.005 cm−1.
DOI: 10.6084/m9.figshare.31154556.v1
title: Rovibrational computations for He2+X2Σu+ including non-adiabatic, relativistic and QED corrections

description: We report the potential energy curve, the diagonal Born-Oppenheimer, non-adiabatic mass, relativistic, and leading-order quantum-electrodynamical (QED) corrections for the ground electronic state of the helium dimer cation; the higher-order QED and finite-nuclear size effects are also estimated. The computations are carried out with an improved error control and over a broader configuration range compared to earlier work [D. Ferenc, V. I. Korobov, and E. Mátyus, Phys. Rev. Lett. 125, 213001 (2020)]. As a result, all rovibrational bound states are reported with an estimated accuracy of 0.005 cm−1.
DOI: 10.5061/dryad.hk2p481
title: Data from: Cytotaxonomy and geographic distribution of cytotypes of species of the South American genus Chrysolaena (Vernonieae, Asteraceae)

description: Understanding speciation and biodiversity patterns in plants requires
 knowledge of the general role of climate in allowing polyploids to escape
 competition and persist with their diploid progenitors. This is a
 particularly interesting issue in widespread species that present multiple
 ploidy levels and occur across a heterogeneous environment. Chrysolaena
 (Vernonieae, Asteraceae) is a cytogenetically very diverse genus, with
 significant interspecific and intraspecific ploidy level variation and
 with continuous distribution across South America. No previous studies
 have summarized chromosome count data of Chrysolaena or addressed the
 cytogeography of the genus. Ploidy level of Chrysolaena species was
 determined by chromosome counting during mitosis and/or meiosis; the
 geographic distribution of cytotypes was examined and the correlations
 between the distribution of particular cytotypes and current ecological
 conditions were evaluated. A total of 43 new chromosome counts and five
 ploidy levels (2x, 4x, 6x, 7x, 8x) were reported. The chromosome number of
 C. cordifolia (2n=7x=70) and a new cytotype for C. propinqua var.
 canescens (2n=4x=40) are reported for the first time. Three geographic
 areas with high diversity of cytotypes and species were detected. The
 results obtained do not suggest a clear distribution pattern that depends
 on climatic factors for Chrysolaena populations. However, a geographic
 pattern was identified in the distribution of ploidy levels, with diploid
 species presenting a more restricted distribution than polyploid species.
description: Chrysolaena
 cytogeographyPopulations of
 Chrysolaena species analysed cytogeographically, with data on ploidy
 levels, geographical coordinates and bioclimatic
 variables.chrysolaena.xlsx
DOI: 10.5061/dryad.6q036
title: Data from: Global test of Eltonian niche conservatism of nonnative freshwater fish species between their native and introduced ranges

description: Despite growing evidence that biotic interactions limit the distribution
 of species and their potential redistribution under climate change, the
 recent surge of interest in niche conservatism has predominantly focused
 on the Grinellian (abiotic) niche, whereas few studies have attempted to
 quantify potential lability in the Eltonian (biotic or trophic) niche.
 Here, we test for conservatism in the Eltonian niche of 32 freshwater fish
 species between their introduced and native ranges from 435 populations
 across the globe. We used stable isotope data to quantify niche shifts
 along the horizontal (δ13C: indicating the origin of the resources
 consumed) and vertical (δ15N: describing the trophic position) dimensions
 of the isotopic niche, as well as shifts in overall isotopic niche
 breadth. Using an assemblage centroid standardized isotope vector analysis
 and controlling for phylogenetic relatedness among species, we
 demonstrated that introduced freshwater fishes exhibited flexibility in
 both resource use and trophic position that was beyond levels of natural
 variability observed in their native ranges. By contrast, niche breadth
 showed variability only within the limits recorded in native populations
 and varied independently from shifts in mean isotopic niche positions.
 Across all species and introduction histories, we found a consistent shift
 towards more balanced acquisition of resources with mixed origins and at
 intermediate trophic positions, suggesting a general mechanism by which
 fish species successfully establish into recipient communities. The
 mechanisms that promote or inhibit species from shifting their Eltonian
 niche remains unknown, but trophic flexibility is likely to contribute to
 both the success and the ecological impacts of invasive species and range
 shifts of native species under future global change.
description: Stable isotopes
 characteristics of the fish species within their native and introduced
 rangestab_dryad.txt
DOI: 10.5061/dryad.c0f2n3mj
title: Data from: Host-jump drives rapid and recent ecological speciation of the emergent fungal pathogen Colletotrichum kahawae

description: Ecological speciation through host-shift has been proposed as a major
 route for the appearance of novel fungal pathogens. The growing awareness
 of their negative impact on global economies and public health created an
 enormous interest in identifying the factors that are most likely to
 promote their emergence in nature. In this work, a combination of
 pathological, molecular and geographic data was used to investigate the
 recent emergence of the fungus Colletotrichum kahawae (Ck). Ck emerged as
 a specialist pathogen causing Coffee Berry Disease in Coffea arabica, due
 to its unparalleled adaptation of infecting green coffee berries. Contrary
 to current hypotheses, our results suggest that a recent host-jump
 underlay the speciation of Ck from a generalist group of fungi seemingly
 harmless to coffee berries. We posit that immigrant inviability and a
 predominantly asexual behavior could have been instrumental in driving
 speciation by creating pleiotropic interactions between local adaptation
 and reproductive patterns. Moreover, we estimate that Ck began its
 diversification at less than 2,200 yrs leaving a very short time frame
 since the divergence from its sibling lineage (∼5,600 yrs), during which a
 severe drop in Ck’s effective population size occurred. This further
 supports a scenario of recent introduction and subsequent adaptation to C.
 arabica. Phylogeographic data revealed low levels of genetic polymorphism
 but provided the first geographically consistent population structure of
 Ck, inferring the Angolan population as the most ancestral and the East
 African populations as the most recently derived. Altogether, these
 results highlight the significant role of host specialization and
 asexuality in the emergence of fungal pathogens through ecological
 speciation.
description: *BEAST and Skyride xml
 filesThis .zip file contains
 the xml input files of the best model for the *BEAST analysis and GMRF
 Skyride.BEAST_xml.zipIMa input and nested models filesThe IMa.zip contains two files: The input file for IMa and the nested models files needed to test competing hypotheses of gene flow patternsIMa.zipSilva2012_alignmentsThis zip files contain the alignments of the six nuclear markers in NEXUS leave format.
DOI: 10.15468/dl.7x6yje
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hydrostachys multifida",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 64 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001065-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.540
title: Data from: Mitochondrial phylogeny of notothenioids: a molecular approach to Antarctic fish evolution and biogeography

description: Antarctic waters represent a unique marine environment delimited by an
 oceanographic barrier, the Polar Front Zone, and characterized by constant
 subzero temperatures and presence of sea ice. A group of teleost fish, the
 Notothenioidei, have adapted to these challenging environmental
 conditions, undergoing a remarkable diversification. In the present study
 a total of 798 base pairs, generated from partial sequencing of 16S and
 12S mitochondrial ribosomal RNA genes, were examined in 33 notothenioid
 species representative of all families included in the suborder
 Notothenioidei. Phylogenetic trees, reconstructed on the basis of sequence
 data using different methods, indicate that traditional hypotheses on
 notothenioid systematics and biogeography might be in need of
 reexamination. Molecular evidence suggests that vicariant speciation could
 be invoked to explain the early divergence of Eleginops maclovinus, a
 species previously included in the family Nototheniidae, which is now
 proposed as the closest sister group to all the rest of notothenioids
 apart from bovichtids. On the other hand, repeated, independent dispersal
 through the Polar Front is proposed for the divergence of other
 subantarctic notothenioid species. Likewise, multiple, independent
 transitions from benthic to pelagic habit are inferred from molecular
 data, at variance with the more conservative hypothesis based on
 cladograms reconstructed from morphological data.
description: Bargelloni et al Data
 Set 1Bargelloni1.nexusBargelloni et al Data Set 2Bargelloni2.nexus
DOI: 10.5061/dryad.bq002
title: Data from: Microsatellite primers for the Pacific Northwest endemic conifer Chamaecyparis lawsoniana (Cupressaceae)

description: Microsatellite primers were developed for the Pacific Northwest conifer,
 Chamaecyparis lawsoniana (A. Murray) Parl. (Cupressaceae), to enhance
 efficiencies in disease-resistance breeding and germplasm screening for
 gene conservation of this rare species. Using multiplexed massively
 parallel Illumina sequencing, we identified over 300,000
 microsatellite-containing sequences from 2 million paired-end microreads.
 After stringent filtering and primer evaluation, we selected 11 primer
 pairs and used these to screen variation in 4 populations of C.
 lawsoniana. Loci show between three and ten repeats per locus, with an
 average of eight. Screening of these markers in the North American
 relative Callitropsis nootkatensis demonstrated limited marker
 transferability, but these markers could have utility in Asian species of
 Chamaecyparis. These genetic markers show high polymorphism and should
 provide a high level of individual discrimination for paternity analysis
 in defined pedigrees, and routine screening of wild variation in
 Chamaecyparis lawsoniana.
description: Jennings_POC_PopInfoThis comma-delimited file provides location and genotype data for individuals from four populations of Oregon Port-Orford cedar that were surveyed with 11 microsatellite loci. The file shows individual numbers, population names, population latitudes, population longitudes, and the microsatellite allele length for diploid loci. Missing genotypes are indicated by the value "0, 0".Jennings_POC_PrimerSeqsThis comma-delimited file provides information for 144 primers that were screened the Port-Orford populations. Included are the primer name, forward and reverse primer sequence, the original sequence name from Illumina sequencing, and the nucleotide sequence of the microread (2 x 80 bp, with read 1 and read 2 separated by 8 N's).