cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8x64f
title: Specialist herbivore performance on introduced plants during native host decline

description: Ash (Fraxinus spp.) is in rapid decline across
 the northeastern USA due to the invasive emerald ash borer (Agrilus
 planipennis Fairmaire). Three recently co-occurring confamilial
 species may serve as alternative larval host plants for ash-reliant
 Lepidoptera. These prospective hosts are non-native shrubs often planted
 in managed suburban landscapes and are sometimes invasive or naturalized
 in North America. Given the imminent decline of ash trees, we considered
 potential downstream effects on insect herbivores historically specialized
 on ash foliage. We measured the performance of three
 ash-specialist hawkmoths (Lepidoptera: Sphingidae)
 on native white ash (Fraxinus americana L.)
 and alternative host plants: common lilac
 (Syringa vulgaris L.), weeping forsythia (Forsythia
 suspensa (Thunb.) Vahl), and European privet (Ligustrum
 vulgare L.). We found the non-native host plants provided varied
 support for larval survival to pupation, with biomass and growth rate
 affected differently by both plant and insect identity. Nearly
 all caterpillars reared on one alternative
 host, European
 privet, exhibited distinct malformations of the
 wing buds at pupation. Given caterpillar presence on privet in the field,
 privet may constitute an ecological trap (i.e., when female moths select a
 sub-optimal host, offspring survival and fitness are reduced). This
 work demonstrates how performance testing can reveal
 species-specific effects of host plant loss on mono- or
 oligophagous insects. For some ash specialists, alternative
 non-native host plants may be suboptimal,
 but some cultivated host plants may
 be able to support certain specialist
 insects during native host decline. We
 suggest that landscaping decisions can be tailored to support
 threatened insect species.
DOI: 10.21338/ess9e03_3
title: ESS9 - integrated file, edition 3.3
DOI: 10.5061/dryad.6djh9w13j
title: Data from: Puercosuchus traverorum n. gen. and sp.: a new malerisaurine azendohsaurid (Archosauromorpha: Allokotosauria) from two monodominant bonebeds in the Chinle Formation (Upper Triassic, Norian) of Arizona

description: Non-archosaur archosauromorphs are a paraphyletic group of diapsid
 reptiles that are important members of global Middle Triassic and Late
 Triassic continental ecosystems. Included in this group are the
 azendohsaurids, a clade of allokotosaurians (kuehneosaurids and
 Azendohsauridae + Trilophosauridae) that retain the plesiomorphic
 archosauromorph postcranial body plan but have evolved disparate cranial
 features that converge on later dinosaurian anatomy, including
 sauropodomorph-like marginal dentition and ceratopsian-like postorbital
 horns. Here we describe a new malerisaurine azendohsaurid from two
 monodominant bonebeds in the Blue Mesa Member, Chinle Formation (Late
 Triassic, ~218–220 Ma); the first occurs at Petrified Forest National Park
 and preserves a minimum of eight individuals of varying sizes, and the
 second occurs near St. Johns, Arizona. Puercosuchus
 traverorum n. gen. and sp. is a carnivorous malerisaurine that is
 closely related to Malerisaurus robinsonae from the
 Maleri Formation of India and to Malerisaurus
 langstoni from the Dockum Group of western Texas. Dentigerous
 elements from Puercosuchus traverorum confirm that some
 Late Triassic tooth morphotypes thought to represent early dinosaurs
 cannot be differentiated from, and likely pertain
 to, Puercosuchus-like malerisaurine taxa. These bonebeds from
 northern Arizona support the hypothesis that non-archosauriform
 archosauromorphs were locally diverse near the middle of the Norian and
 experienced an extinction event prior to the end-Triassic mass extinction
 coincidental with the Adamanian-Revueltian boundary recognized at
 Petrified Forest National Park. The relatively late age of this
 early-diverging taxon (Norian) suggests that the diversity of
 azendohsaurids is underrepresented in the Middle Triassic and Late
 Triassic fossil records around the world.
DOI: 10.26165/juelich-data/alicti
title: Open-sourced renewable energy potential analysis for Japan

description: Zenodo. The repository stores code, land-use dataset, and reverse-viewshed maps to calculate capacity potential for Offshore Wind, Onshore Wind, and Open-field PV in Japan for the base scenario and under visibility restriction from important landscapes. The code use ETHOS.GLAES (https://github.com/FZJ-IEK3-VSA/glaes) for land eligibility analysis and capacity potential calculation under the open-source workflow ETHOS.REFLOW (https://github.com/FZJ-IEK3-VSA/ethos.REFLOW).
DOI: 10.5061/dryad.7wm37pvwb
title: Stellaria motuoensis (Caryophyllaceae), a new species from Xizang, China

description: Stellaria motuoensis sp. nov. (Caryophyllaceae) is described and
 illustrated as a new species from Xizang of China on the basis of both
 morphological and molecular evidence. Phylogenetic analysis based on ITS
 sequence data show that S. motuoensis is closely related to S. monosperma.
 Morphological observation has shown that S. motuoensis is most similar to
 S. monosperma var. paniculata, but readily differs by its bisexual flower
 with no petals (versus bisexual or unisexual with petals 5), five stamens
 (versus 5 or 10), filiform roots (versus fusiform, thick, fleshy), terete
 stem (versus quadrangular), stems glabrous basally, pubescent apically
 (versus glandular pubescent, with 1 or 2 rows of hairs above), leaves
 glabrous (versus pubescent).
DOI: 10.5061/dryad.pnvx0k6q0
title: Even short-term revegetation complicates soil food webs and strengths their links with ecosystem functions

description: Degradation of dryland ecosystems is a worldwide problem caused by climate
 change and human activities. To restore these degraded ecosystems,
 governments have implemented projects that often include revegetation, but
 we still lack an understanding of how soil food webs and ecosystem
 functions are affected by revegetation. By conducting a large-scale
 revegetation experiment under two degradation intensities (low and high)
 on the Inner Mongolian degraded grassland, we tested the effects of
 revegetation on primary producers (plants), key components of soil food
 webs (bacteria, fungi, and nematodes), and ecosystem functions (soil C and
 N mineralization). After 4 years, revegetation greatly increased the
 biomass of plants and soil bacteria and fungi but had less effects on soil
 nematode functional groups. Revegetation increased vegetation and
 bacterial diversities and soil C and N mineralization rates, altered the
 structures of vegetation and soil microbial communities, but did not
 affect fungal or nematode diversity. The stronger effects of revegetation
 on plants, soil bacteria, soil fungi, and soil nematodes in plots with low
 degradation intensity than in plots with high degradation intensity
 indicated that future revegetation efforts should consider the degree of
 degradation. Revegetation also increased the interactions among plants,
 soil food webs, and ecosystem functions, indicating that the
 revegetation-induced changes in soil food webs could facilitate the
 recovery of soil nutrients and vegetation productivity in degraded
 grasslands. Synthesis and applications. Overall, the effects of
 revegetation were stronger on plants (primary producers) and soil
 microorganisms (intermediate trophic levels) than on soil nematodes
 (higher trophic levels), and even short-term revegetation increased the
 complexity of soil food webs and strengthened their relationships with
 soil functions in degraded grasslands. These results highlight the effects
 of restoration on multiple trophic levels in degraded drylands, and
 suggest that some aspects of plant-soil interactions in global drylands
 could be rapidly improved by appropriate restoration.
DOI: 10.5061/dryad.r2280gbfq
title: Temporal correlations among demographic parameters are ubiquitous but highly variable across species

description: Temporal correlations among demographic parameters can strongly
 influence population dynamics. Our empirical knowledge, however,
 is very limited regarding the direction and the magnitude of these
 correlations and how they vary among demographic parameters and species’
 life-histories. Here, we use long-term demographic data from 15 bird and
 mammal species with contrasting pace of life to quantify correlation
 patterns among five key demographic parameters: juvenile and adult
 survival, reproductive probability, reproductive success and productivity.
 Correlations among demographic parameters were ubiquitous, more frequently
 positive than negative, but strongly differed across species. Correlations
 did not markedly change along the slow-fast continuum of life-histories,
 suggesting that they were more strongly driven by ecological than
 evolutionary factors. As positive temporal demographic correlations
 decrease the mean of the long-run population growth rate, the common
 practice of ignoring temporal correlations in population models could lead
 to the underestimation of extinction risks in most species.
DOI: 10.5061/dryad.ht76hdrj2
title: Imaging the onset of oscillatory signaling dynamics during mouse embryo gastrulation

description: A fundamental requirement for embryonic development is the coordination of
 signaling activities in space and time. A notable example in vertebrate
 embryos is found during somitogenesis, where gene expression oscillations
 linked to the segmentation clock are synchronized across cells in the
 presomitic mesoderm (PSM) and result in tissue-level wave patterns. To
 examine their onset during mouse embryo development, we studied the
 dynamics of the segmentation clock gene Lfng during gastrulation. To this
 end, we established an imaging setup using selective plane illumination
 microscopy (SPIM) that enables culture and simultaneous imaging of up to
 four embryos (SPIM-for- 4). Using SPIM-for-4, combined with genetically
 encoded signaling reporters, we detected the onset of Lfng oscillations
 within newly formed mesoderm at presomite stages. Functionally, using
 chemical inhibition and genetic mutants, we found that initial synchrony
 and first ~6-8 oscillation cycles occurred even when Notch-signaling was
 impaired, revealing similarities to previous findings made in zebrafish
 embryos. Finally, we show that a spatial period gradient is already
 present at the onset of oscillatory activity, providing a potential
 mechanism accounting for our observation that wave patterns build up
 gradually over the first oscillation cycles.
DOI: 10.5061/dryad.nvx0k6dvh
title: Visual complexity of egg patterns predicts egg rejection according to Weber's law

description: Visual complexity is ubiquitous in nature. Drivers of complexity include
 selection in coevolutionary arms races between antagonists. However, the
 causes and consequences of biological complexity and its perception are
 largely understudied, partly because complexity is difficult to quantify.
 Here, we address this by studying egg pattern complexity and its
 perception in hosts (tawny-flanked prinia Prinia subflava ), which
 visually recognize and reject mimetic eggs of their virulent brood
 parasite (cuckoo finch Anomalospiza imberbis ). Using field data and an
 optimization algorithm, we compute a complexity metric which predicts
 rejection of experimentally placed conspecific eggs in prinia nests. Real
 cuckoo finch eggs exhibit significantly lower pattern complexity than
 prinia eggs, suggesting that high complexity benefits hosts because it
 distinguishes host eggs from parasitic eggs. We show that prinias perceive
 complexity differences according to Weber's law of proportional
 processing (i.e. relative, rather than absolute, differences between
 stimuli are processed in discrimination, such that two eggs with simple
 patterns are more easily discriminable than two with complex patterns).
 This may influence coevolutionary trajectories of hosts and parasites. The
 new methods presented for quantifying complexity and its perception can
 help us to understand selection pressures driving the evolution of
 complexity and its consequences for species interactions.
description: The dataset provided includes raw data of complexity scores for
 eggs in the field, and egg rejection data from field experiments carried
 out in 2007-2009 and 2018-2020.
DOI: 10.5061/dryad.zpc866tb2
title: Supplementary material and supplementary data files for: Handling logical character dependency in phylogenetic inference: Extensive performance testing of assumptions and solutions using simulated and empirical data

description: Logical character dependency is a major conceptual and methodological
 problem in phylogenetic inference of morphological datasets, as it
 violates the assumption of character independence that is common to all
 phylogenetic methods. It is more frequently observed in higher-level
 phylogenies or in datasets characterizing major evolutionary transitions,
 as these represent parts of the tree of life where (primary) anatomical
 characters either originate or disappear entirely. As a result, secondary
 traits related to these primary characters become “inapplicable” across
 all sampled taxa in which that character is absent. Various solutions have
 been explored over the last three decades to handle character dependency,
 such as alternative character coding schemes and, more recently, new
 algorithmic implementations. However, the accuracy of the proposed
 solutions, or the impact of character dependency across distinct
 optimality criteria, has never been directly tested using standard
 performance measures. Here, we utilize simple and complex simulated
 morphological datasets analyzed under different maximum parsimony
 optimization procedures and Bayesian inference to test the accuracy of
 various coding and algorithmic solutions to character dependency. This is
 complemented by empirical analyses using a recoded dataset on
 palaeognathid birds. We find that in small, simulated datasets, absent
 coding performs better than other popular coding strategies available
 (contingent and multistate), whereas in more complex simulations (larger
 datasets controlled for different tree structure and character
 distribution models) contingent coding is favored more frequently. Under
 contingent coding, a recently proposed weighting algorithm produces the
 most accurate results for maximum parsimony. However, Bayesian inference
 outperforms all parsimony-based solutions to handle character dependency
 due to fundamental differences in their optimization procedures—a simple
 alternative that has been long overlooked. Yet, we show that the more
 primary characters bearing secondary (dependent) traits there are in a
 dataset, the harder it is to estimate the true phylogenetic tree,
 regardless of the optimality criterion, owing to a considerable expansion
 of the tree parameter space.
description: All data and codes to produce all simulated datasets, empirical
 dataset, run analyses, produce output trees, and generate tables, graphs
 and plots. See more details in README file.
DOI: 10.5061/dryad.83bk3j9tn
title: The effects of antibiotic combination treatments on Pseudomonas aeruginosa tolerance evolution and coexistence with Stenotrophomonas maltophilia

description: Pseudomonas aeruginosa bacterium is a common pathogen of Cystic Fibrosis
 (CF) patients due to its ability to evolve resistance to antibiotics
 during treatments. While P. aeruginosa resistance evolution is well
 characterised in monocultures, it is less well understood in polymicrobial
 CF infections. Here, we investigated how exposure to ciprofloxacin,
 colistin, or tobramycin antibiotics, administered at sub-MIC doses alone
 and in combination, shaped the tolerance evolution of P. aeruginosa (PAO1
 lab and clinical CF LESB58 strains) in the absence and presence of a
 commonly co-occurring species, Stenotrophomonas maltophilia. Increases in
 antibiotic tolerances were primarily driven by the presence of that
 antibiotic in the treatment. We observed a reciprocal cross-tolerance
 between ciprofloxacin and tobramycin, and when combined these antibiotics
 selected increased MICs for all antibiotics. Though the presence of S.
 maltophilia did not affect the tolerance or the MIC evolution, it drove P.
 aeruginosa into extinction more frequently in the presence of tobramycin
 due to its relatively greater innate tobramycin tolerance. In contrast, P.
 aeruginosa dominated and drove S. maltophilia extinct in most other
 treatments. Together, our findings suggest that besides driving high-level
 antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter
 competitive bacterial interactions, leading to target pathogen extinctions
 in multi-species communities.
description: See Methods in paper for collection. MIC values (MIC data.csv)
 derived from visual inspection of antibiotic growth measurements plotted
 as a growth curve. Optical density data has been
 blank-corrected, and in the case of the antibiotic growth measurements
 (Antibiotic growth data.csv) averaged over ≤3 technical
 replicates.
DOI: 10.26165/juelich-data/qrilm3
title: Reverse viewshed analysis for a priori landscape impacts assessment of renewable infrastructure

description: Zenodo. The repository stores code to generate cumulative reverse viewshed maps that shows theoretically visible area for large-scale onshore wind and open-field PV placements from list of important viewpoints or landscapes. The generated cumulative reverse viewshed maps can be used as additional exclusion area in land eligibility analysis (LEA) for placements of onshore wind and open-field PV invisible from the selected important landscapes. The code can be run on GRASS-GIS environment and can be parallelized on an HPC. Take a look at the README for further software requirements and steps to work with example datasets.
DOI: 10.5061/dryad.5dv41ns7p
title: Basil leaf traits

description: Microbial inoculations or “biofertilizers” represent novel contributions
 to sustainable agriculture. While belowground mechanisms surrounding how
 biofertilizers enhance crop production are well described, their role in
 aboveground trait expression remains less well explored. We quantified
 infraspecific variation in Leaf Economics Spectrum (LES) traits in
 response to 10 biofertilizer treatments in basil (Ocimum basiclicum)
 cultivated under hydroponic conditions. Multiple physiological (i.e.,
 maximum photosynthesis rates (A), dark respiration (R), leaf-level light
 compensation points (LLCP)) and morphological traits (i.e., leaf mass per
 area (LMA), leaf thickness) varied significantly across microbial
 treatments. Following treatments, basil plants differentiated from one
 another along an infraspecific LES, with certain plants expressing more
 resource acquiring LES trait values (i.e., high A, R, leaf N, and low
 LMA), vs. others that expressed the opposite suite of resource conserving
 LES trait values. Infraspecific trait covariation largely matched LES
 patterns observed among plants globally. Multivariate and hierarchical
 analyses further revealed that certain treatments—namely those including
 Bacillus sp. strains—increased leaf resource capture traits such as A and
 leaf N. Biofertilizers influence plant performance through a role in
 moderating infraspecific leaf trait variation, thereby suggesting
 aboveground leaf traits may be used to diagnose optimal biofertilizer
 formulations in basil and other crops.
description: Data was collected on plants growing in hydropnic conditions,
 using an LI-6800 portable infrared gas analyzer, along with elemental
 analysis.
DOI: 10.15468/dl.sypz2y
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus dislineatus"
 ]
}

 The dataset includes 46 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003102-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vhhmgqnwc
title: Phylogenetic study of the New Caledonian endemic genus Adenodaphne (Lauraceae) confirms its synonymy with Litsea

description: The genus Adenodaphne is currently considered endemic to New Caledonia,
 but its distinction from Litsea is questionable based on morphological
 similarity. An earlier phylogenetic analysis (ITS) including one species
 of Adenodaphne and two Asian species of Litsea did support their close
 relationship but did not permit resolution of their generic boundary. We
 sampled the four species of Adenodaphne currently recognized (11
 accessions) and 11 of the 13 endemic species of Litsea currently
 recognized, plus one undescribed species (24 accessions in total). Based
 on our extensive herbarium studies, field work, and especially our
 molecular phylogenetic analyses (ITS) we conclude that Adenodaphne is not
 distinct from Litsea and that all species of Adenodaphne should be
 recognized within Litsea, thereby necessitating the creation of two new
 species synonymies and one nomen novum. As well, Litsea paoueensis is here
 synonymized with L. deplanchei.
description: In this study we generated internal
 transcribed spacer region (ITS) sequence data for 43 new samples
 (<em>Litsea</em>, 31; <em>Adenodaphne</em>, 11;
 <em>Actinodaphne</em>, 1). We selected the ITS region as it
 has been successfully used across the Lauraceae at different taxonomic
 levels (Chanderbali et al. 2001; Jian-Feng et al. 2016; Li et al. 2004; Li
 et al. 2008; Li et al. 2011; Liu et al. 2013; Rohde et al. 2017), and
 provides the highest level of resolution at the species level (China Plant
 Bol Group et al. 2011; Liu et al. 2017). Thirty-three samples were collected in New
 Caledonia, six during an expedition in Papua New Guinea (see Munzinger et
 al. 2020), one in New Zealand, and one in Wallis and Futuna. The New
 Caledonian samples represent the four species of
 <em>Adenodaphne</em> accepted by Kostermans in the Flore as
 well as eleven of the thirteen <em>Litsea</em> species that he
 considered there, plus two individuals from Ouaième, that we could not
 relate to any <em>Litsea</em> or
 <em>Adenodaphne</em> species described. We also included ITS
 sequences from GenBank from published studies that included vouchered
 specimens, among them that of the type species for the genus
 <em>Litsea</em>, <em>L. glutinosa</em> (Lour.)
 C.B.Rob. We did not include <em>Litsea</em> paoueensis, known
 only from the type Hürlimann 1158, or <em>Litsea</em>
 <em>imbricata</em> Guillaumin (known only from two
 collections), both of which we searched for in the field in vain. As well,
 we excluded <em>L. mackeei</em> Kosterm., which Kostermans
 (1977) described 3 years after the publication of his treatment in the
 Flore, as it belongs to the Oleaceae (Munzinger and McPherson 2017). All
 taxa are listed in Table 1, which includes the code of the herbarium
 (sensu Thiers 2021) where the vouchers are deposited.
description: All samples included in this study are vouchered. Please
 acknowledge the collector and collector number when using these
 samples.