cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tb2rbp00x
title: Air temperatures overpredict changes to stream fish assemblages with climate warming compared to water temperatures

description: Studies predicting how the distribution of aquatic organisms will shift
 with climate change often use projected increases in air temperature or
 water temperature. However, the assumed correlations between water
 temperature change and air temperature change can be problematic,
 especially for mountainous, high elevation streams. Using stream fish
 assemblage data from 1,442 surveys across a mountain - plains gradient
 (Wyoming, USA; 1990-2018), we compared the responsiveness of thermal
 guilds, native status groups, and assemblage structure to projected
 climate warming from generalized air temperature models and
 stream-specific water temperature models. Air temperature models
 consistently predicted greater range shift differences between warm-water
 and cold-water species, with air temperatures predicting greater increases
 in occurrence and greater range expansions for warm-water species. The
 “over-prediction” of warm-water species expansions resulted in air
 temperature models predicting higher rates of novel species combinations,
 greater increases in local species richness, and higher magnitudes of
 biotic homogenization compared with water temperature models. Despite
 differences in model predictions for warm-water species, both air and
 water temperature models predicted that three cold-water species would
 exhibit similar decreases in occurrence (decline of 1.0% and 1.8% of sites
 per 1 °C warming, respectively) and similar range contractions (16.6 and
 21.5 m elevation loss per 1 °C warming, respectively). The
 “over-prediction” for warm-water species is partially attributable to
 water temperatures warming at slower rates than air temperatures because
 local, stream-scale factors (e.g., riparian cover, groundwater inputs)
 buffer high elevation streams from rising air temperatures. Our study
 provides the first comparison of how inferences about climate-induced
 biotic change at the species- and assemblage-levels differ when modeling
 with generalized air temperatures versus stream-specific water
 temperatures. We recommend future studies use stream-specific water
 temperature models, especially for mountainous, high elevation streams, to
 avoid the “over-prediction” of biotic changes observed from air
 temperature variables.
description: <strong>Database on species distributions and environmental
 characteristics (csv) </strong> Information on
 species distributions and environmental characteristics of the 1,442
 sample sites used for modeling in this study.
 <strong>Description of the database used for distribution
 modeling (word)</strong> Metadata describing the
 structure of the excel database used for species distribution
 modeling.
DOI: 10.5061/dryad.dv41ns1z8
title: Evolution of chromosome number in wild onions (Allium, Amaryllidaceae)

description: Polyploidy has been shown to be a significant driver of diversification
 among land plants.  In addition to whole-genome duplication,
 other common mechanisms of chromosome number evolution include increases
 by a multiple of 1.5 in chromosome number due to the fusion of gametes
 with different ploidy levels (demi-polyploidy), gains or losses of single
 chromosomes that alter the DNA content of an organism (aneuploidy), or
 chromosome fission or fusion (ascending dysploidy or descending dysploidy,
 respectively).  Considering the high variability in chromosome
 number transitions across multiple clades within angiosperms and the
 ancient genome duplication events responsible for their diversity, more
 studies of large polyploid systems are necessary to close the gaps in
 understanding chromosomal evolution in polyploid plants.  Allium
 (Amaryllidaceae) is an ideal candidate for polyploid research because it
 is a large clade that includes numerous natural populations of diploid and
 polyploid species.  Species of Allium mainly occupy temperate
 climates in the Northern Hemisphere and include economically important
 ornamentals and cultivated crops such as leeks, garlic, chives, and
 onions.  Here, we used a global molecular phylogeny of Allium to
 examine chromosomal evolution with chromEvol v. 2.0 which uses
 likelihood-based methods for inferring the pattern of chromosome number
 change across a phylogeny.  The best-fit model of chromosomal
 evolution indicated that chromosome transitions within Allium occurred
 through the constant gains and losses of single chromosomes as well as
 demi-polyploidization events, with the rate of chromosome gain events
 being approximately 2.5 to 4.5 times more likely to occur than
 demi-polyploidization and loss events, respectively.
DOI: 10.5061/dryad.w6m905qpm
title: Spatial pattern of genetic diversity in field populations of Fusarium incarnatum-equiseti species complex

description: Fusarium is associated with a number of wilt, blight, scab and rot
 diseases in a range of economically important staple food crops worldwide.
 An assessment of the genetic structure and population stratification of
 Fusarium incarnatum-equiseti species complex (FIESC) pathogen populations
 is important to understand the evolutionary potential of such populations
 in adapting to environmental change. Based on inter-simple sequence repeat
 polymerase chain reaction (ISSR-PCR), it was found that the pathogen
 population was structured into three genetic clusters for which genetic
 differentiation was higher within than among populations. There was high
 intra-population genetic diversity for population 1 (94.63%) which
 consisted largely of isolates collected from North Trinidad. Populations 2
 and 3 had a low level of admixture among the populations based on overall
 population differentiation. Population 1 accounted for the highest amount
 of genetic variation (95.82%) followed by populations 2 and 3. Population
 stratification was reflected in the dendrogram topology, which consisted
 of three main genetic clusters and which coincided with the outcome of
 Bayesian and PCoA analyses. The populations were isolated by distance and
 Voronoi tessellations indicated physical or structural barriers to gene
 flow which contributed to restricted admixture between two of three
 populations. These findings suggest a high evolutionary potential for this
 FIESC pathogen population, the implications of which directly affect
 disease management strategies.
description: This data was analyzed using a number of different population
 genetics and phylogenetic software including GenAlEx, STRUCTURE and
 STRUCTURE HARVESTER, POPGENE, POPS, TESS, PAST4 and MEGA
description: For Population Genetics Analyses using GenAlEx 6.5 software as an
 add-in in Excel, there are 2 .xlsx files: 1) PCoA -
 principle components analysis: this is the datasheet that was prepared
 using the ISSR binary matrix. Specifically datasheet "PCoA-dist
 std" applies - Principle components analysis using genetic
 distance 2) Mantels test of isolation by distance: this
 is the datasheet that was prepared for estimating Mantel's test.
 Specifiically the datasheet "GGDvGD MT (2)" applies - Genetic
 geographic distance by genetic distance Mantel's test
 All column and datasheet abbreviations can be found in the
 GenAlEx 6.5 software manual using the link below: 
 https://biology-assets.anu.edu.au/GenAlEx/Download_files/GenAlEx%206.5%20Guide.pdf
DOI: 10.5061/dryad.q2bvq83jq
title: A tale of two conifers: Migration across a dispersal barrier outpaced regional expansion from refugia

description: Aim: Understanding how climate refugia and migration over great distances
 have facilitated species survival during past climate changes is crucial
 for evaluating contemporary threats to biodiversity, particularly in the
 face of dispersal barriers. We address this longstanding question on the
 refugial origins and post-glacial development of mesic forests. Location:
 Pacific Northwest, North America. Taxon: Mountain hemlock (Tsuga
 mertensiana) and western redcedar (Thuja plicata) Methods: Range-wide
 genotyping-by-sequencing (ddRADseq) of both study species and a pollen
 reconstruction of mountain hemlock presence over the last 20,000 years.
 Results: Mountain hemlock occurred in two coastal populations (Oregon and
 Washington) during the glacial maximum, each of which dispersed to the
 interior (Idaho and British Columbia) during the Holocene. These
 populations spread in the direction of dominant winds across a barrier of
 dry, rain-shadowed valleys. In contrast, for western redcedar, we infer
 four disparate refugia during the glacial maximum: southern (California),
 central (Washington), interior (Idaho), and northern (Haida Gwaii
 islands). Main conclusions: Despite the presence of pre-dispersed refugial
 populations, the majority of the redcedar distribution was colonized by
 the central population. The history for these two key conifers contrast
 with many recent studies emphasizing the role of cryptic refugia in
 colonizing modern species ranges.
DOI: 10.25338/b8ms7n
title: Data from: Wolbachia in the spittlebug Prosapia ignipectus: variable infection frequencies, but no apparent effect on host reproductive isolation

description: Animals serve as hosts for complex communities of microorganisms,
 including endosymbionts that live inside their
 cells. Wolbachia bacteria are perhaps the most common
 endosymbionts, manipulating host reproduction to propagate. Many Wolbachia
 cause cytoplasmic incompatibility (CI), which results in reduced egg hatch
 when uninfected females mate with infected males. Wolbachia that
 cause intense CI spread to high and relatively stable frequencies, while
 strains that cause weak or no CI tend to persist at intermediate, often
 variable, frequencies. Wolbachia could also contribute to host
 reproductive isolation (RI), although current support for such
 contributions is limited to a few systems. To test for Wolbachia frequency
 variation and effects on host RI, we sampled several local Prosapia
 ignipectus (Fitch)(Hemiptera: Cercopidae) spittlebug populations in the
 northeastern USA over two years, including closely juxtaposed Maine
 populations with different monomorphic color forms, “black” and “lined”.
 We discovered a group-B Wolbachia (wPig) infecting P. ignipectus
 that diverged from group-A Wolbachia—like model wMel and wRi
 strains in Drosophila—6 to 46 MYA. Populations of the sister species
 Prosapia bicincta (Say) from Hawaii and Florida are uninfected, suggesting
 that P. ignipectus acquired wPig after their initial divergence. wPig
 frequencies were generally high and variable among sites and between
 years. While phenotyping wPig effects on host reproduction is not
 currently feasible, the wPig genome contains three divergent sets of CI
 loci, consistent with high wPig frequencies. Finally, Maine monomorphic
 black and monomorphic lined populations of P. ignipectus share both wPig
 and mtDNA haplotypes, implying no apparent effect of wPig on the
 maintenance of this morphological contact zone. We hypothesize P.
 ignipectus acquired wPig horizontally as observed for many Drosophila
 species, and that significant CI and variable transmission produce high
 but variable wPig frequencies.
description: This data archive contains the scripts, raw and basecalled
 Nanopore reads and assemblies used for the phylogenetic analyses, plus the
 infection status data from the accompanying manuscript (Wheeler et al.
 2021, in press). A detailed description of the contents is provided in the
 README.txt file.
DOI: 10.5061/dryad.xpnvx0kfq
title: Biomass allocation in response to salinity and competition in native and invasive species

description: Biomass allocation to different plant parts affects the subsequent capture
 rate of resources and reproduction. Thus, many studies have been conducted
 on the biomass allocation to learn growth, reproduction and competitive
 ability of plants. However, few researches have explored how biomass
 allocation responses to non-resource factor and interspecific competition
 over time. We experimentally investigated the effects of soil salinity and
 competition on root:shoot ratio (RS), reproductive effort (RE; seed
 biomass:total biomass ratio), the relationship between belowground and
 aboveground biomass, the relationship between reproductive and vegetative
 biomass, growth, and reproduction of invasive Spartina alterniflora and
 native Phragmites australis. The biomass of P. australis decreased with
 increasing salinity, whereas that of S. alterniflora did not significantly
 change. The reproduction of P. australis decreased with increasing
 salinity under competitive conditions, and that of S. alterniflora
 increased. Therefore, P. australis was less-tolerant, and S. alterniflora
 was more-tolerant. The RS of P. australis increased over time under
 competitive conditions and with increasing salinity, and that of S.
 alterniflora did not significantly change. The RE of P. australis
 decreased to zero with decreasing total biomass, and that of S.
 alterniflora did not significantly correlate with total biomass. Both
 species exhibited a linear relationship between belowground and
 aboveground biomass. The relationship between reproductive and vegetative
 biomass in P. australis was linear, and the reproductive biomass of S.
 alterniflora did not significantly correlate with the vegetative biomass.
 Competitive dominance shifted from P. australis to S. alterniflora with
 increasing salinity. The findings demonstrated that the plastic biomass
 allocation of less-tolerant species facilitates performance of
 less-tolerant species in favorable environments, while the fixed biomass
 allocation of more-tolerant species facilitates performance of
 more-tolerant species in stressful environments, suggesting that S.
 alterniflora invasion driven by competitive exclusion probably occur in
 high salinity zones, and reproductive ability of invasive species should
 be relatively stronger during exclusion. More broadly, linking level of
 environmental stresses with tolerance of plants is crucial to
 understanding and predicting the biomass allocation and its effects on
 plant performance, which is an expansion of predictions from optimal
 theory and allometric theory and therefore illustrates the conditionality
 of these predictions.
DOI: 10.5061/dryad.66t1g1k27
title: Combined responses of primary coral polyps and their algal endosymbionts to decreasing seawater pH

description: With coral reefs declining globally, resilience of these ecosystems hinges
 on successful coral recruitment. However, knowledge of the acclimatory
 and/or adaptive potential in response to environmental challenges such as
 ocean acidification (OA) in earliest life stages is limited. Our
 combination of physiological measurements, microscopy, computed tomography
 techniques and gene expression analysis allowed us to thoroughly elucidate
 the mechanisms underlying the response of early life stages of corals,
 together with their algal partners, to the projected decline in oceanic
 pH. We observed extensive physiological, morphological and transcriptional
 changes in surviving recruits, and the transition to a
 less-skeleton/more-tissue phenotype. We found that decreased pH conditions
 stimulate photosynthesis and endosymbiont growth, and gene expression
 potentially linked to photosynthates translocation. Our unique holistic
 study discloses the previously unseen intricate net of interacting
 mechanisms that regulate the performance of these organisms in response to
 OA.
description: The readme file contains an explanation of each variable in the
 dataset. Information on how the measurements were done can be found in the
 associated manuscript referenced above.
DOI: 10.5061/dryad.5tb2rbp40
title: Data from: Quantifying variation in female internal genitalia: no evidence for plasticity response to sexual conflict risk in a seed beetle

description: Sexually antagonistic coevolution can drive the evolution of male traits
 that harm females, and female resistance to those traits. While males have
 been found to vary their harmfulness to females in response to social
 cues, whether female resistance traits vary in response to social cues
 remains to be examined. Among seed beetles, male genital spines harm
 females during copulation and females might resist male harm via
 thickening of the reproductive tract walls. Here we develop a novel
 Micro-CT imaging technique to quantify female reproductive tract thickness
 in 3-dimensional space. We compared the reproductive tracts of female
 Callosobruchus maculatus from populations that had evolved under high and
 low levels of sexual conflict, and for females reared under a social
 environment that predicted either high or low levels of sexual conflict.
 We show that neither social environment nor evolutionary history
 significantly affected reproductive tract thickness. Our novel methodology
 allows for the measurement of fine-scale changes in the internal female
 reproductive tract, and will allow future investigations into the internal
 organs of insects and other animals.
description: <strong>Wyber_et_al_2021_Script</strong>
 R script containing all analyses.
 <strong>CT-Data</strong> Raw data
 analysed in: "Quantifying variation in female internal genitalia: no
 evidence for plasticity response to sexual conflict risk in a seed
 beetle". The first sheet contains the raw data, and the second
 contains a legend.
 <strong>Repeatability</strong> Raw
 data used in repeatability analysis in: "Quantifying variation in
 female internal genitalia: no evidence for plasticity response to sexual
 conflict risk in a seed beetle". The first sheet contains the raw
 data, and the second contains a legend.
 <strong>FijiScript1</strong>
 Script used in the program "Fiji". See main document
 for full instruction manual.
 <strong>FijiScript2</strong>
 Script used in the program "Fiji". See main document
 for full instruction manual.
 <strong>FijiScript3</strong>
 Script used in the program "Fiji". See main document
 for full instruction manual.
DOI: 10.5061/dryad.j0zpc86dw
title: Grazing-induced biodiversity loss impairs grassland ecosystem stability at multiple scales

description: Livestock grazing is a major driver shaping grassland biodiversity,
 functioning, and stability. Whether grazing impacts on grassland
 ecosystems are scale-dependent remains unclear. Here, we conducted a
 sheep-grazing experiment in a temperate grassland to test grazing effects
 on the temporal stability of productivity across scales. We found that
 grazing increased species stability, but substantially decreased local
 community stability due to reduced asynchronous dynamics among species
 within communities. The negative effect of grazing on local community
 stability propagated to reduce stability at larger spatial scales. By
 decreasing biodiversity both within and across communities, grazing
 reduced biological insurance effects and hence the up-scaling of stability
 from species to communities and further to larger spatial scales. Our
 study provides the first evidence for the scale-dependence of grazing
 effects on grassland stability through biodiversity. We suggest that
 ecosystem management should strive to maintain biodiversity across scales
 to achieve sustainability of grassland ecosystem functions and services.
description: All the response variables have been natural log-transformed.
 They are unitless, except for "d_abun" with a percentage
 (%).
DOI: 10.5061/dryad.dz08kprxj
title: Data from: Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species

description: Since the last revision in 2015, the taxonomy of section Flavipedes
 evolved rapidly along with the availability of new species delimitation
 techniques. This study aims to re-evaluate the species boundaries of
 section Flavipedes members using modern delimitation methods applied to an
 extended set of strains (n=90) collected from various environments. The
 analysis used DNA sequences of three house-keeping genes (benA, CaM, RPB2)
 and consisted of two steps: application of several single-locus (GMYC,
 bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to
 sort the isolates into putative species, which were subsequently validated
 using DELINEATE software that was applied for the first time in fungal
 taxonomy. As a result, four new species are introduced, i.e. A.
 alboluteus, A. alboviridis, A. inusitatus and A. lanuginosus, and A.
 capensis is synonymized with A. iizukae. Phenotypic analyses were
 performed for the new species and their relatives and the results showed
 that the growth parameters at different temperatures and colonies
 characteristics were useful for differentiation of these taxa. The revised
 section harbors 18 species, most of them are known from soil. However,
 common species from the section are ecologically diverse, occurring in
 indoor environment (6 species), clinical samples (5 species), food and
 feed (4 species), droppings (4 species) and other less common
 substrates/environments. Due to the occurrence of section Flavipedes
 species in the clinical material/hospital environment, we also evaluated
 the susceptibility of 66 strains to six antifungals (Amphotericin B,
 Itraconazole, Posaconazole, Voriconazole, Isavuconazole, Terbinafine)
 using the reference EUCAST method. These results showed some potentially
 clinically relevant differences in susceptibility between species. For
 example, MICs higher than those observed for wild-type A. fumigatus were
 found for both triazoles and amphotericin B for A. ardalensis, A. iizukae,
 and A. spelaeus whereas A. lanuginosus, A. luppiae, A. movilensis, A.
 neoflavipes, and A. olivimuriae were comparable to or more susceptible as
 A. fumigatus. Finally, terbinafine was in vitro active against all species
 except A. alboviridis.