cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mpg4f4qxt
title: Phylogenetically diverse diets favor more complex venoms in North American pitvipers

description: The role of natural selection in the evolution of trait complexity can be
 characterized by testing hypothesized links between complex forms and
 their functions across species. Predatory venoms are traits composed of
 multiple proteins that collectively function to incapacitate prey. Venom
 complexity fluctuates considerably over evolutionary timescales, with
 apparent increases and decreases in complexity, yet the evolutionary
 causes of this variation is unclear. Here, we tested alternative
 hypotheses for the link between venom complexity and ecological sources of
 selection related to diet in the largest clade of front-fanged
 venomous snakes in North America: the rattlesnakes, copperheads, cantils,
 and cottonmouths Crotalus, Sistrurus and Agkistrodon. We generated
 independent transcriptomic and proteomic measures of venom complexity and
 then estimated prey diversity using the past century's extensive
 natural history studies on these snakes. We then conducted comparative
 tests relating  different measures of predator venom complexity
 and prey community diversity using the first, genome-scale, dated
 phylogenies for this clade of snakes. Strikingly, phylogenetic diversity
 of prey was more strongly correlated to venom diversity than was species
 diversity, implicating prey species divergence, rather than the number of
 lineages alone, in the evolution of venom complexity. This positive
 relationship was observed within three of the four largest toxin gene
 families in viper venom. Given documented examples of taxonomic
 specificity of venoms spanning several levels of divergence,
 we suggest that the phylogenetic diversity of prey measures
 functionally-relevant divergence in the molecular targets of
 venom, a claim supported by diversity in the coagulation cascade targets
 of snake venom serine proteases. Our results support the general
 concept that the evolved diversity of species in an ecological community
 is more important than their overall number in determining evolutionary
 patterns in predator trait complexity.
description: Venom-gland transcriptomes were subject to Trinity assembly and
 BUSCO v.3 search for orthologous genes. Alignments were produced using
 MAFFT and trimmed with trim-al. See manuscript for additional
 details.
DOI: 10.15468/dl.4944gb
title: Occurrence Download

description: A dataset containing 9619 records in GBIF matching the query:
SELECT
 '448' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 71.92889702835036
 AND decimalLongitude &lt;= 81.82717519335071
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 9619 records were derived from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002698-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kd51c5b4n
title: The influence of climate and paleoclimate on distributions of global conifer clades depends on geographic range size

description: Aim: We investigate how plant distributions are
 shaped by current and paleoclimate regimes. We
 specifically use global conifer biodiversity to test
 if paleoclimatic signatures are stronger in
 range-restricted taxa compared
 to widespread taxa.  Location: Global
 Taxon: Coniferales Methods: We combine global geographic
 occurrences for 606 conifer species and 69 conifer genera with climate
 information (modern day and paleoclimate) to examine predictors of current
 conifer distribution. We test how climate predicts richness of
 range-restricted taxa and influences turnover of widespread taxa using
 generalized dissimilarity models and a zeta diversity framework. We also
 construct ensemble distribution models to test if paleoclimates
 differentially influence the current distribution of range-restricted
 versus widespread taxa.    
 Results: Generalized dissimilarity models suggest
 that paleoclimatic variation in precipitation and
 temperature are associated with differences in richness of small-range
 species and genera; most of these taxa occur in areas of high climatic
 stability. Turnover among more widespread taxa, especially genera, is
 related to broad temperature gradients, including both modern climate
 and paleoclimatic variation in climate. Ensemble
 distribution models also suggest that paleoclimatic variation contributes
 more to the current range of genera with restricted ranges.  Main
 conclusions: The most widespread conifers broadly follow past and
 current temperature gradients, leading to latitudinal sorting of genera
 based on their physiological adaptations. Range-restricted species and
 genera, however, preferentially occur in climatically stable regions,
 where they contribute to high richness hotspots. History, rather than
 current climate patterns, likely exerts a disproportionate influence on
 global patterns of richness in the group. 
description: The data provided here include latitude and longitude occurrence
 points collected from GBIF and herbarium locations (methods used to
 collate and download points decribed in Sundaram et al.
 2019-https://doi.org/10.1098/rspb.2019.1887).
 Spreadsheet titled 'Occurrence points' provides
 the following information: FID =
 ID number/ observation number Name = Short 5-8 letter
 code indicating which conifer species the occurrence point is
 for lon = longitude in degrees (rounded to 1/10th
 decimal) lat = latitude in degrees (rounded to 1/10th
 decimal) species = Conifer binomial name for
 the occurrence point; binomial name is recorded
 as Genus_species
DOI: 10.5061/dryad.63xsj3v1n
title: Randomized Study of Bedside vs Hallway Rounding: Neurology Rounding Study

description: Over the last century, attending rounds have shifted away from the
 bedside. Despite evidence for greater patient satisfaction rates and
 improved nursing perception of teamwork with bedside presentations,
 medical residents and attending physicians are apprehensive of the bedside
 approach. There is a lack of data to guide rounding practices within
 neurology, and therefore optimal rounding methods remain unclear. The
 objective of this study was to compare bedside rounding with hallway
 rounding on an academic neurology inpatient service and assess efficiency,
 trainee education, and satisfaction among patients and staff. We conducted
 a single-center prospective randomized study of bedside versus hallway
 rounding on new inpatient neurology admissions over one-week blocks. The
 bedside team presented patients at the bedside, while the hallway team
 presented patients outside of the patient’s room. We evaluated the two
 approaches with time-motion analysis, which investigated the rounding
 style’s effect on composition and timing of rounds (primary outcome), and
 surveys of patients, nurses, residents, and attending physicians on both
 teams (secondary outcomes). The mean rounding time per newly admitted
 patient in the bedside group (n = 38 patients) and hallway group (n = 41
 patients) was 23 minutes and 23.2 minutes, respectively (p = 0.93). The
 bedside group spent on average 56.4% of patient rounding time in the
 patient’s room, while the hallway group spent 39.5% of rounding time in
 the patient’s room (p = 0.036). Residents perceived hallway rounding to be
 more efficient and associated it with a superior educational experience
 and more effective data review. Nurses had improved perception of their
 participation in bedside rounds. Though patients’ views of bedside and
 hallway rounds were similar, patients who had experienced bedside rounds
 preferred it. In conclusion, bedside rounding was perceived less favorably
 by most residents but was as efficient as hallway rounding. Although
 bedside rounding limited the use of technology for data review, it
 promoted nursing participation and resulted in more time spent with the
 patient. --
DOI: 10.15468/dl.d6mu2q
title: Occurrence Download

description: A dataset containing 488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Dryobalanops aromatica"
 ]
}

 The dataset includes 488 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002708-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7272/q6gx48sv
title: Persistence of ambigrammatic narnaviruses requires translation of the reverse open reading frame

description: Narnaviruses are RNA viruses detected in diverse fungi, plants, protists,
 arthropods and nematodes. Though initially described as simple single-gene
 non-segmented viruses encoding RNA-dependent RNA polymerase (RdRp), a
 subset of narnaviruses referred to as “ambigrammatic” harbor a unique
 genomic configuration consisting of overlapping open reading frames (ORFs)
 encoded on opposite strands. Phylogenetic analysis supports selection to
 maintain this unusual genome organization, but functional investigations
 are lacking. Here, we establish the mosquito-infecting Culex narnavirus 1
 (CxNV1) as a model to investigate the functional role of overlapping ORFs
 in narnavirus replication. In CxNV1, a reverse ORF without homology to
 known proteins covers nearly the entire 3.2 kb segment encoding the RdRp.
 Additionally, two opposing and nearly completely overlapping novel ORFs
 are found on the second putative CxNV1 segment, the 0.8 kb “Robin” RNA. We
 developed a system to launch CxNV1 in a naïve mosquito cell line, then
 showed that functional RdRp is required for persistence of both segments,
 and an intact reverse ORF is required on the RdRp segment for persistence.
 Mass spectrometry of persistently CxNV1-infected cells provided evidence
 for translation of this reverse ORF. Finally, ribosome profiling yielded a
 striking pattern of footprints for all four CxNV1 RNA strands that was
 distinct from actively-translating ribosomes on host mRNA or co-infecting
 RNA viruses. Taken together, these data raise the possibility that the
 process of translation itself is important for persistence of
 ambigrammatic narnaviruses, potentially by protecting viral RNA with
 ribosomes, thus suggesting a heretofore undescribed viral tactic for
 replication and transmission.
DOI: 10.5061/dryad.xsj3tx9dg
title: Increasing flavonoid concentrations in root exudates enhance associations between arbuscular mycorrhizal fungi and an invasive plant

description: Many invasive plants have enhanced mutualistic arbuscular mycorrhizal (AM)
 fungal associations, however, mechanisms underlying differences in AM
 fungal associations between introduced and native populations of invasive
 plants have not been explored. Here we test the hypothesis that variation
 in root exudate chemicals in invasive populations affects AM fungal
 colonization and then impacts plant performance. We examined flavonoids
 (quercetin and quercitrin) in root exudates of native and introduced
 populations of the invasive plant Triadica sebifera and tested their
 effects on AM fungi and plant performance. We found that plants from
 introduced populations had higher concentrations of quercetin in root
 exudates, greater AM fungal colonization and higher biomass. Applying root
 exudates more strongly increased AM fungal colonization of target plants
 and AM fungal spore germination when exudate donors were from introduced
 populations. The role of root exudate chemicals was further confirmed by
 decreased AM fungal colonization when activated charcoal was added into
 soil. Moreover, addition of quercetin into soil increased AM fungal
 colonization, indicating quercetin might be a key chemical signal
 stimulating AM fungal associations. Together these results suggest genetic
 differences in root exudate flavonoids play an important role in enhancing
 AM fungal associations and invasive plants’ performance, thus considering
 root exudate chemicals is critical to unveiling mechanisms governing
 shifting plant-soil microbe interactions during plant invasions.
DOI: 10.5061/dryad.fbg79cnt3
title: Data from: Variations in ratio and loads of soil nitrogen and phosphorus explain the coexistence of dominant tree species in a boreal forest of Xinjiang, northwest China

description: The resource ratio hypothesis (RRH) and the nutrient-load hypothesis (NLH)
 state that species coexistence is driven by the ratios and loads
 (contents) of multiple limiting resources, respectively. However, roles of
 resource ratios and loads to mature forest ecosystems remains unclear.
 Data were collected within 300 quadrats (20m×20m) spread across a 12 ha
 plot of boreal forest in the Kanas of Xinjiang, northwest China. We used
 torus translation tests to analyze the associations of dominant tree
 species with specific microhabitats. The linear mixed models were used to
 assess effects of resource ratios and contents on abundance and basal area
 of specific species, as well as within different life stages. Two
 shade-tolerant species, Picea obovata and Pinus
 sibirica, exhibited opposite relationships to the spatial
 distribution of soil nitrogen (N) content and phosphorus (P)
 content. Picea. obovata was associated with
 microhabitats with high N:P ratio, while P.
 sibirica preferred microhabitats with low N:P ratio. The
 light-demanding trees, Betula pendula clustered at both low N and P sites.
 Another light-demanding trees, Larix sibirica, did not show any
 significant habitat preferences. Moreover, N:P ratio mainly affected
 species abundance, while their contents largely impacted basal area of
 species. And effects of N:P ratio or contents on species distribution
 showed a decreasing trend from sapling to adults. Overall, our findings
 indicate that niche partitioning caused by resource variations may
 alleviate interspecific competition and contribute to the species
 coexistence, providing convincing proof for the importance of resource
 ratio and load on maintaining diversity in boreal forests.
DOI: 10.5061/dryad.z08kprrbj
title: A multi-tiered sequence capture strategy spanning broad evolutionary scales: application for phylogenetic and phylogeographic studies of orchids

description: With over 25,000 species, the drivers of diversity in the Orchidaceae
 remain to be fully understood. Here we outline a multi-tiered sequence
 capture strategy aimed at capturing 100’s of loci to enable phylogenetic
 resolution from subtribe to subspecific levels in orchids of the tribe
 Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to
 give five target sequence sets aimed at the tribe (Sets 1 & 2),
 subtribe (Set 3), and within subtribe levels (Sets 4 & 5).
 Analysis included alternative de novo and
 reference-guided assembly, before target sequence extraction, annotation
 and alignment, and application of a
 homology-aware k-mer block phylogenomic approach, prior
 to phylogenetic inference using maximum-likelihood. Our evaluation
 considered 87 taxa in two test datasets: 67 samples spanning the tribe,
 and 72samples involving 24 closely
 related Caladenia species. The tiered design achieved
 high target loci recovery (&gt;89%), with the median number of
 recovered loci in Sets 1–5 as follows: 212, 219, 816, 1024, and 1009,
 respectively. Interestingly, as a first test of
 the homologous k-mer approach for targeted
 sequence capture data, our study revealed its potential for enabling
 robust phylogenetic species tree inferences. Specifically, we found
 matching, and in one case improved phylogenetic resolution within species
 complexes, compared to conventional phylogenetic analysis involving target
 gene extraction. Our findings indicate that a customised
 multi-tiered sequence capture strategy, in combination with promising yet
 under-utilized phylogenomic approaches, will be effective for
 groups where interspecific divergence is recent, but information on deeper
 phylogenetic relationships is also required.
description: Please see the full publication in Molecular Ecology Resources
 along with the Online Supplementary material.  See also the Readme file
 (Peakall MER-20-0380 Dyrad Readme.pdf) in this repository for info on the
 data structure.
DOI: 10.5061/dryad.6t1g1jwxq
title: A habenula-insular circuit encodes the willingness to act

description: The decision that it is worth doing something rather than nothing is a
 core yet understudied feature of voluntary behaviour. Here we study
 “willingness to act”, the probability of making a response given the
 context. Human volunteers encountered opportunities to make effortful
 actions in order to receive rewards, while watching a movie inside a 7T
 MRI scanner. Reward and other context features determined willingness-
 to-act. Activity in the habenula tracked trial-by-trial variation in
 participants’ willingness-to-act. The anterior insula encoded individual
 environment features that determined this willingness. We identify a
 multi-layered network in which contextual information is encoded in the
 anterior insula, converges on the habenula, and is then transmitted to the
 supplementary motor area, where the decision is made to either act or
 refrain from acting via the nigrostriatal pathway.
description: To use the dataset please see Guideline.docx
DOI: 10.5061/dryad.ht76hdrdn
title: Enhancing ecosystem services in apple orchards: Nest boxes increase pest control by insectivorous birds

description: Ecological intensification in croplands aims to enhance biodiversity-based
 ecosystem services, helping to increase yield while reducing agricultural
 environmental impacts. Identifying ecological intensification tools of
 wide applicability and easily implemented by farmers is, therefore, an
 imperative. Here, we verify the efficiency of provisioning artificial nest
 boxes for insectivorous birds to reinforce pest biological control in
 apple orchards. The study was conducted in 24 cider-apple orchards in
 Asturias (NW Spain) over three years. We compared the effect of
 insectivorous birds between orchards with and without nest boxes occupied
 by different bird species, through insectivory estimates based on attack
 on a sentinel pest and measurements of arthropod abundance in apple trees.
 We also identified preys that birds of different species captured to feed
 nestlings. Bird occupancy of nest boxes was widespread, ranging 25.0-33.3%
 each year. Great tit was the dominant species, followed by blue tit and,
 occasionally, common redstart. Predation pressure on apple pests increased
 in orchards with nest boxes, as judged by the increased proportion of
 sentinel models attacked by birds (34.9% increase in 2018 and 41.1% in
 2019), decreased biomass of tree-dwelling arthropods (-51.7%) and reduced
 probability of apple pest occurrence (from 57 to 40%), compared to
 orchards without nest boxes. Nesting species showed different predatory
 roles in apple orchards. Fewer attacks on sentinel pests but lower
 arthropod biomass was associated with blue tit rather than great tit.
 Besides, blue tit fed nestlings at a faster rate and included in their
 diet a higher proportion of apple pests than great tit, which preyed
 mostly on other herbivorous insects. Synthesis and applications. We
 demonstrated the usefulness of nest boxes for insectivorous birds in
 enhancing biological control of apple pests at a regional scale,
 identifying tit species as complementary predators of apple pests and
 herbivores. From the farmers’ perspective, providing nest boxes in
 orchards may represent an efficient, easy to implement, cheap and
 attractive measure of ecological intensification, compatible with other
 actions fostering biodiversity in croplands.
DOI: 10.5061/dryad.66t1g1k19
title: Data from: Dyadic leader-follower dynamics change across situations in captive house sparrows

description:  Individuals can behave as either leaders or followers in many
 taxa of collectively-moving animals. Leaders initiate movements and may
 incur predation risks while followers are thought to be more risk-averse.
 As a group encounters different challenges and ecological situations,
 individuals in the group may change their social role. We investigated
 leader and follower roles using dyads of captive house sparrow (Passer
 domesticus) during both exploration of a novel environment and a
 simulation of predator attack. During the exploration of a novel
 environment individuals behaved consistently either as leaders or
 followers. However, in the simulated attack tests, individuals in the
 dyads switched their roles, with ‘followers’ leading the escape flights
 and ‘leaders’ following them. Our study provides evidence of (i)
 consistent differences between individuals in behavior during social
 escape and (ii) a relationship between social roles
 across different situations. We suggest that such relationship hinges on
 individual risk-taking tendencies, which manifest through different social
 roles across different ecological situations. We further speculate that
 risk-taking individuals might gain benefits by following risk-averse
 individuals during an escape flight.
DOI: 10.5061/dryad.vhhmgqnrv
title: Effects of cultivation practice on floristic and flowering diversity of spontaneously growing plant species on arable fields

description: In the past, the floristic diversity of arable fields has been described
 in terms of species diversity (SD) and their degree of coverage (C), but
 never in combination with the recording of the actually flowered species
 (FS) and their flowering intensity (FI) to striking differences in the
 cultivation methods on arable land. In relation with SD and C, however, FS
 and FI may provide important additional information on the functional
 biodiversity of fields. The aim was therefore to investigate the effects
 of a) conventional, b) organic  as well as c) smallholder (never
 application of herbicides) on the floristic diversity. Using a region in
 Germany, we investigated SD, C, FS and FI synchronously in a), b) and c),
 by 356 vegetation surveys (5x5m plots) conducted in spring and summer in
 2019 in winter cereals. Statistical tests were used to analyse the
 differences between a), b) and c). The medians were used to compare the
 floristic diversity of a), b) and c) and finally relationships of FS and
 FI to SD were analysed in relation to the cultivation methods. Significant
 differences in SD, C, FS and FI were found between the a), b) and c) in
 spring and summer characterised by sharp declines from c) to b) to a). A
 drastic reduction in floristic diversity from c) 100 to b) 52 to a) 3 was
 determined. Plants in flower (FS, FI), were very poorly in a), moderately
 well to well in b) and well to very well represented in c). C) to a) was
 characterised by an sharp decline, and, from a) to b) by sharp increase in
 floristic diversity. With current acreage proportions of a) in mind, this
 would affect, about one-third of land area in Germany, associated with a
 drastic reduction in functional biodiversity for insects.
description: Collected: field investigations, vegetation surveys
 Processed: statistical data analysis by the use of statistics
 software R (R Core Team, 2020)