cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.05qfttf1n
title: Larger pollinators deposit more pollen on stigmas across multiple plant species – a meta-analysis

description: Abstract 1. Many insect species provide essential pollination services.
 However, the amount of pollen deposited onto a stigma when visiting a
 flower (“single visit pollen deposition”, SVD) can vary greatly among taxa
 depending on morphological traits of pollinators. Further, SVD is commonly
 measured using one of two methods (‘static’: waiting for an insect to
 visit a flower present on plant, and ‘active’: removing the flower and
 presenting it to a flower visitor) that may also differ in their
 effectiveness. 2. To gain a more comprehensive understanding of how SVD
 compares among pollinators, we conducted a hierarchical meta-analysis
 using data from 28 studies identified by a systematic review. These
 contained SVD data for 94 bee and 33 fly taxa (hereafter “wild
 pollinators”), across 30 plant species from which we included 127
 observations. In the analysis of each study, we used the western honey bee
 (Apis mellifera) as a comparator species. 3. Wild pollinators deposited
 more pollen onto stigmas per single visit than honeybees, and those with
 larger body deposited significantly more pollen than smaller ones. Of the
 two methodological approaches to assess SVD, ‘static’ versus ‘active’, we
 found no significant difference regarding the amount of deposited pollen.
 4. Synthesis and applications. Our meta-analysis highlights the breadth of
 wild pollinators that contribute to pollination effectiveness via their
 delivery of pollen to many crop and non-crop plant species. However, just
 25% of the observations assessed the amount of pollen deposited by fly
 species. Our findings point to the need to further quantify the
 pollination effectiveness of non-bee pollinators as studies have largely
 focused on managed and wild bee species.
DOI: 10.5061/dryad.zcrjdfn95
title: Data from: Mosses reduce soil nitrogen availability in a subarctic birch forest via effects on soil thermal regime and sequestration of deposited nitrogen

description: In high-latitude ecosystems, bryophytes are important drivers of ecosystem
 functions. Alterations in abundance of mosses due to global change may
 thus strongly influence carbon (C) and nitrogen (N) cycling and hence
 cause feedback on climate. The effects of mosses on soil microbial
 activity are, however, still poorly understood. Our study aims at
 elucidating how and by which mechanisms bryophytes influence microbial
 decomposition processes of soil organic matter and thus soil nutrient
 availability. We present results from a field experiment in a subarctic
 birch forest in northern Sweden, where we partly removed the moss cover
 and replaced it with an artificial soil cover for simulating moss effects
 on soil temperature and moisture. We combined this with a fertilization
 experiment with 15N-labelled N for analyzing the effects of moss
 N-sequestration on soil processes. Our results demonstrate the capacity of
 mosses to reduce soil N availability and retard N cycling. The comparison
 with artificial soil cover plots suggests that the effect of mosses on N
 cycling is linked to the thermal insulation capacity of mosses causing low
 average soil temperature in summer and strongly reduced soil temperature
 fluctuations, the latter also leading to a decreased frequency of
 freeze-thaw events in autumn and spring. Our results also showed, however,
 that the negative temperature effect of mosses on soil microbial activity
 was in part compensated by stimulatory effects of the moss layer, possibly
 linked to leaching of labile substrates from the moss. Furthermore, our
 results revealed that bryophytes efficiently sequester added N from wet
 deposition and thus prevent effects of increased atmospheric N deposition
 on soil N availability and soil processes. Synthesis. Our study emphasizes
 the important role of mosses in carbon and nutrient cycling in high
 latitude ecosystems and the potential strong impacts of reductions in moss
 abundance on microbial decomposition processes and nutrient availability
 in subarctic and boreal forests.
DOI: 10.25338/b8zs7r
title: Davis Amtrak station pilot project evaluation

description: This study investigates barriers to accessing the Davis Amtrak Station to
 inform a program designed to increase access to the station with on-demand
 alternatives. The program aims to decrease private vehicle use to access
 the station and for travel to locations outside of Davis through
 partnerships with a carpool/rideshare app, as well as a ridehail app.
 Motivations for the program stem from the high passenger usage at the
 Davis station that may be impacted by parking capacity and other
 challenges. The city has limited interest in or ability to add new parking
 capacity, however pricing will be introduced to the lot in the future. Due
 to the COVID-19 pandemic, the City has not yet set a launch date for the
 program. This report evaluates the potential for the program using survey
 data collected from Davis residents about their travel expectations once
 COVID-19 is no longer a threat. The results of this study provide insights
 into residents’ interest in the planned pilot programs. Residents are most
 likely to use a free ridehail program to travel to the train station,
 while some are also likely to use a carpool/rideshare program and/or a
 free shuttle to downtown. Those with higher perceived risks associated
 with riding the train during COVID-19 are less likely to use these
 programs. City planners are already considering these issues, and these
 results underscore the importance of these issues in the final design and
 outreach for this pilot program.
description: The data was collected through an online survey.
 The data has been minimally processed; removel of unusable
 responses, computation of new variables, and removal of all identifying
 information for participants.
DOI: 10.25338/b8v33d
title: Phylogenomic species delimitation in the ants of the Temnothorax salvini Group (Hymenoptera: Formicidae): An integrative approach

description: The members of the Temnothorax salvini species group are
 rarely collected, arboreally nesting ants of Central American forests.
 Previously thought to consist of two broadly dispersed species, recent
 collections have revealed a diversity of specimens that defy the
 two-species salvini group concept, but these are
 difficult to distinguish from each other based solely on morphology. I
 contrast several model-based approaches to species delimitation based on
 target-enriched genomic data. With molecular data from thousands of
 ultraconserved elements (UCEs), mitochondrial genome sequences, and
 morphometric data, I use an integrated approach to species delimitation
 within the salvini group. Morphometric data were
 analyzed using cluster analysis of principal component analysis (PCA)
 output. I use several popular methods of molecular species delimitation,
 including bPTP, BPP, and STACEY, using a novel approach to filtering UCE
 data based on posterior predictive checks of nucleotide substitution model
 adequacy. Additionally, I use iBPP to integrate morphometric PCA data and
 filtered UCE data in a ‘total evidence’ analysis. I use geographical range
 data for an independent contrast to discriminate amongst competing species
 delimitation hypotheses. Furthermore, I investigate the evolutionary
 timescale and biogeographical history of the group and find that it
 evolved roughly 12.5 Ma ago in habitats associated with present day
 mid-to-high elevations of the mountain complex spanning southern Mexico to
 northern Nicaragua. Additionally, dispersal of
 the salvini group into the Southern Sierra Madre in
 Mexico, lowland habitats, and the Sierra de Talamanca in Costa Rica and
 Panama subsequent to mountain building in southern Central America 5-8 Ma
 ago appears to follow a taxon-cycle dynamic, with the
 lowland-adapted T. aztecus representing the most recent
 expansion phase. I find that the salvini group, which
 previously contained two named species, is composed of nine, all of which
 are morphologically diagnosable a posteriori.
description: See the README file for a synopsis of the contents of the
 dataset.
DOI: 10.5061/dryad.wstqjq2jq
title: Geranylgeraniol prevents zoledronic acid-mediated reduction of viable mesenchymal stem cells via induction of Rho-dependent YAP activation

description: Long-term use of zoledronic acid (ZA) increases the risk of
 medication-related osteonecrosis of the jaw (MRONJ). This may be
 attributed to ZA-mediated reduction of viable mesenchymal stem cells
 (MSCs). ZA inhibits protein geranylgeranylation, thus suppressing cell
 viability and proliferation. Geranylgeraniol (GGOH), which is a naturally
 found intermediate compound in the mevalonate pathway, has positive
 effects against ZA. However, precise mechanisms by which GGOH may help
 preserve stem cell viability against ZA are not fully understood. The
 objective of this study was to investigate the cytoprotective mechanisms
 of GGOH against ZA. The results showed that while ZA dramatically
 decreased the number of viable MSCs, GGOH prevented this negative effect.
 GGOH-rescued ZA-exposed MSCs formed mineralization comparable to that
 produced by normal MSCs. Mechanistically, GGOH preserved the
 number of viable MSCs by its reversal of ZA-mediated Ki67+ MSC
 number reduction, cell cycle arrest and apoptosis. Moreover, GGOH
 prevented ZA-suppressed RhoA activity and YAP activation. The results also
 established the involvement of Rho-dependent YAP and YAP-mediated CDK6 in
 the cytoprotective ability of GGOH against ZA. In
 conclusion, GGOH preserves a pool of viable MSCs with osteogenic
 potency against ZA by rescuing the activity of Rho-dependent YAP
 activation, suggesting GGOH as a promising agent and YAP as a
 potential therapeutic target for MRONJ.
DOI: 10.5061/dryad.66t1g1k11
title: Idiopathic normal pressure hydrocephalus with synucleinopathy: diagnosis and treatment

description: Pearls  -    Idiopathic normal
 pressure hydrocephalus (iNPH) is characterized by the classic triad of
 gait disturbance, urinary incontinence, and cognitive impairment in the
 presence of ventriculomegaly without known risk factors for communicating
 hydrocephalus. Shunt surgery is indicated for iNPH patients who respond to
 the removal of CSF.  Oy-sters -    The
 striatal dopaminergic deficit on dopamine transporter (DAT) scan is not
 uncommon in patients with iNPH, which might be related to an unfavorable
 long-term outcome of shunt surgery. For iNPH patients with clinical
 features suggesting synucleinopathy such as REM sleep behavior disorder,
 DAT scan could be considered to identify concurrent synucleinopathy before
 shunt surgery.  -    Repeated removal
 of CSF could be considered as an alternative treatment instead of shunt
 surgery in iNPH patients who are ineligible for shunt surgery or have
 sustained improvement after CSF removal.
DOI: 10.5281/zenodo.18396263
title: AI Assistants Textual Echo Chambers
DOI: 10.5061/dryad.9s4mw6mf7
title: Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade-specific evolutionary processes

description: Aim: Historical processes that shaped current diversity patterns of
 seaweeds remain poorly understood. Using Dictyotales, a globally
 distributed order of brown seaweeds as a model, we test if historical
 biogeographical and diversification patterns are comparable across clades.
 Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora
 and Padina, are exceptionally diverse. Specifically we test if the
 evolutionary processes in these clades that shaped their latitudinal
 diversity patterns are in line with the tropical conservatism, the
 out-of-the-tropics, and diversification rate hypotheses. Location: Global
 coastal benthic marine environments. Taxon: Dictyotales (Phaeophyceae)
 Methods: Species diversity was inferred using DNA-based species
 delineation, addressing cryptic diversity and circumventing taxonomic
 problems. A six-gene time-calibrated phylogeny, distribution data of 3,755
 specimens, and probabilistic modeling of geographic range evolution was
 used to infer historical biogeographical patterns. The phylogeny was
 tested against different trait dependent models in order to compare
 diversification rates for different geographical units as well as
 different thermal affinities. Results: The Dictyotales originated in the
 Middle Jurassic and reach a current peak of species diversity in the
 Central Indo-Pacific. Ancestral range estimation points to a southern
 hemisphere origin of Dictyotales corresponding to the tropical southern
 Tethys Sea. Our results demonstrate that diversification rates were
 generally higher in tropical regions, but increased diversification rates
 in different clades are driven by different processes. Three major clades
 underwent a major diversification burst in the early Cenozoic, with
 Dictyota and Padina expanding their distribution into temperate regions,
 while Lobophora retained a predominantly tropical niche. Main conclusions:
 Our results are consistent with both the tropical conservatism hypothesis,
 in which clades originate and remain in the tropics (Lobophora), and the
 out-of-the-tropics scenario, where taxa originate and expand towards the
 temperate regions while preserving their presence in the tropics
 (Dictyota, Padina).
description: The "Dictyotales ML tree JBI-20-0060.Tre" file contains
 the Dictyotales species tree based on Maximum likelihood
 analysis. The "Time tree JBI-20-0060.tre"
 file contains the time-tree resulting from the BEAST analysis.
 The "Biogeobears R script JBI-20-0060.r" file contains
 the script for the BioGeoBEARS analysis. The
 "biogeobears_regions.txt" file is the
 input files for the BioGeoBEARS analysis.
DOI: 10.5061/dryad.t4b8gtj0p
title: Asymmetric interspecific competition drives shifts in signalling traits in fan-throated lizards

description: Interspecific competition can occur when species are unable to distinguish
 between conspecific and heterospecific mates or competitors when they
 occur in sympatry.  Selection in response to
 interspecific competition can lead to shifts in signalling traits - a
 process termed as agonistic character displacement. In two fan-throated
 lizard species- Sitana laticepsand Sarada
 darwini, females are morphologically indistinguishable and male
 agonistic signalling behaviour is similar. Consequently, in areas where
 these species overlap, males engage in interspecific aggressive
 interactions. To test whether interspecific male aggression
 between S. laticeps and S.
 darwini results in agonistic character displacement, we
 quantified species recognition and signalling behaviour using staged
 encounter assays with both conspecifics and heterospecifics across
 sympatric and allopatric populations of both species. We found an
 asymmetric pattern, wherein males of S. laticepsbut
 not S. darwini showed differences in competitor
 recognition and agonistic signalling traits (morphology and behaviour) in
 sympatry compared to allopatry. This asymmetric shift in traits is likely
 due to differences in competitive abilities between species and can
 minimize competitive interactions in zones of sympatry. Overall, our
 results support agonistic character displacement, and highlight the role
 of asymmetric interspecific competition in driving shifts in social
 signals.
DOI: 10.6078/d1vh87
title: nIRCat characterization and acute brain slice imaging

description: Dopamine neuromodulation of neural synapses is a process implicated in a
 number of critical brain functions and diseases. Development of protocols
 to visualize this dynamic process is essential to understanding how
 dopamine modulates neurochemical brain function. We have developed a
 non-genetically encoded, near infrared (nIR) catecholamine nanosensor
 (nIRCat) capable of identifying ~2 µm dopamine release hotspots in the
 dorsal striatal brain slices. This platform is readily introduced into
 both genetically tractable and intractable organisms and is compatible
 with a number of dopamine receptor agonist and antagonists. In the
 following work, we describe the synthesis, characterization, and
 implementation of nIRCat in brain slices. We show how to image
 electrically and optogenetically stimulated dopamine release using nIRCat,
 and how these imaging protocols can be adapted to study the effects of
 dopamine receptor pharmacology. We also detail the development of
 video-analysis software to identify and track the location and kinetics of
 dopamine release hot spots over the course of nIRCat imaging experiments.
 Altogether, synthesis and characterization of nIRCat takes 5 hours and
 imaging live brain slices takes 6 hours. 
description: These data were collected using absorbance spectroscopy,
 fluorescence spectroscopy, and wide-field near-infrared fluorescence
 microscopy
description: All data includes metadata files outlining the details of the
 data and experiment.
DOI: 10.5061/dryad.xksn02vf0
title: Data from: Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

description: A recent study argued that coalescent-based models of species delimitation
 mostly delineate population structure not species, and called for the
 validation of candidate species using biological information additional to
 the genetic information, such as phenotypic or ecological data. Here we
 introduce a framework to interrogate genomic datasets and coalescent-based
 species trees for the presence of candidate species in situations where
 additional biological data are unavailable, unobtainable, or
 uninformative. For de novo genomic studies of species boundaries, we
 propose six steps: (a) visualize genetic affinities among individuals to
 identify both discrete and admixed genetic groups from first principles,
 and to hold aside individuals involved in contemporary admixture for
 independent consideration; (b) apply phylogenetic techniques to identify
 lineages; (c) assess diagnosability of those lineages as potential
 candidate species; (d) interpret the diagnosable lineages in a geographic
 context (sympatry, parapatry, allopatry); (e) assess significance of
 difference or trends in the context of sampling intensity; and (f) adopt a
 holistic approach to available evidence to inform decisions on species
 status in the difficult cases of allopatry. We use this approach to
 distinguish candidate species from within-species lineages for a
 widespread species complex of Australian freshwater fishes (Retropinna
 spp.). Our framework addresses two cornerstone issues in systematics that
 are often not explicitly discussed in genomic species discovery:
 diagnosability and how to determine it, and what criteria should be used
 to decide whether diagnosable lineages are conspecific or represent
 different species.
description: Sequencing for the SNP dataset was performed using DArTseq™
 (Diversity Arrays Technology Pty Ltd, Canberra Australia). We extracted
 genomic DNA for the Sanger sequencing from muscle tissue from each
 specimen using the DNeasy Tissue Kit (QIAGEN Inc., Chatsworth CA) or by
 phenol-chloroform extraction. The allozyme dataset for the original study
 on the composite taxon MTV (TAS, ADM, and MDB) was extended to include a
 further 149 smelt from 16 additional sites from the relevant region of
 observed admixture (southern Victoria and Murray River).  Refer to
 Materials and Methods of the main body of the paper and in Supplementary
 Materials.
description: Refer to the README file.
DOI: 10.5061/dryad.0cfxpnw0m
title: The genus Diaphanosoma (Diplostraca: Sididae) in Greece: Morphological and molecular assessment

description: For the genus Diaphanosoma Fischer (Cladocera) the species’ name “D.
 brachyurum” has been widely used for many decades to identify other
 species belonging to this genus. To clarify the diversity of the genus in
 Greek lakes in the present study we morphologically and genetically
 identified the Diaphanosoma species occurring in eight lakes. Three
 hundred twenty-nine Diaphanosoma individuals were morphologically examined
 while for the genetic analyses the mtDNA COI gene was sequenced in 48
 individuals. Combining the morphological and genetic results, we verified
 the occurrence of D. mongolianum, D. orghidani and D. macedonicum in our
 study area. We could not confirm prior records of D. brachyurum and D.
 lacustris while we provide the molecular identity of D. macedonicum.
 Furthermore, we highlight the need to check whether the European D.
 mongolianum populations are characterised of mitochondrial discordance and
 hybridization as the individuals from the Asian type locality of the
 species. Our results support the importance of combining both approaches
 to correctly identify taxonomic species, despite the extra effort and cost
 during the sample analysis.
description: <strong>Diaphanosoma
 microphotographs</strong> This file contains
 cladoceran microphotographs analysed for the morphological analysis of the
 species identified in the manuscript
 <strong>Supplementary Tables S1-S4.
 </strong> <strong>Supplementary_Figure
 1_ABGD analysis</strong>
DOI: 10.5061/dryad.c59zw3r60
title: Data from: Impact of male trait exaggeration on sex-biased gene expression and genome architecture in a water strider

description: Background: Exaggerated secondary sexual traits are widespread in nature
 and often evolve under strong directional sexual selection. Although
 heavily studied from both theoretical and empirical viewpoints, we have
 little understanding of how sexual selection influences sex-biased gene
 regulation during the development of exaggerated secondary sexual
 phenotypes, and how these changes are reflected in genomic architecture.
 This is primarily due to the limited availability of representative
 genomes and associated tissue- and sex-transcriptomes to study the
 development of these traits. Here we present the genome and developmental
 transcriptomes, focused on the legs, of the water strider Microvelia
 longipes, a species where males exhibit strikingly long third legs
 compared to females, which they use as weapons. Results: We generated a
 high-quality genome assembly with 90% of the sequence captured in 13
 scaffolds. The most exaggerated legs in males were particularly enriched
 in both sex-biased and leg-biased genes, indicating a specific signature
 of gene expression in association with trait exaggeration. We also found
 that male-biased genes showed patterns of fast evolution compared to
 non-biased and female-biased genes, indicative of directional or relaxed
 purifying selection. By contrast to male-biased genes, female-biased genes
 that are expressed in the third legs, but not the other legs, are
 over-represented in the X chromosome compared to the autosomes. An
 enrichment analysis for sex-biased genes along the chromosomes revealed
 also that they arrange in large genomic regions or in small clusters of
 two to four consecutive genes. The number and expression of these enriched
 regions were often associated with the exaggerated legs of males,
 suggesting a pattern of common regulation through genomic proximity in
 association with trait exaggeration. Conclusion: Our findings indicate how
 directional sexual selection may drive sex-biased gene expression and
 genome architecture along the path to trait exaggeration and sexual
 dimorphism.
description: # Data from: Impact of male trait exaggeration on sex-biased gene
 expression and genome architecture in a water strider
 [https://doi.org/10.5061/dryad.c59zw3r60](https://doi.org/10.5061/dryad.c59zw3r60) ## Description of the data and file structure Oct-24 Version: We added a separate GTF data file for the genome annotation of Microvelia longipes See separate README file for further details. Supplementary online information for Toubiana, Armisen et al. BMC Biology 2021