cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8sf7m0ctb
title: Data from: Ecological trait divergence over evolutionary time underlies the origin and maintenance of tropical spider diversity

description: Relative to its size, tropical Asia is likely to be the richest region in
 terms of biodiversity. However, the factors of species diversity formation
 and maintenance in Southeast (SE) Asia and neighboring regions remain
 poorly understood. Here we infer the evolutionary relationships within
 psilodercid spiders by incorporating fossil information into a robust,
 unprecedentedly complete species-level phylogeny of 202 extant species to
 explore potential abiotic drivers and ecological features underlying their
 stable diversification history. The combination of extant and extinct
 historical biogeographic data indicates that in situ speciation is the
 predominant form of diversification in tropical Asia but diverse
 Cretaceous psilodercids in Myanmar ambers were replaced by other
 biogeographical lineages during the northward movements of the Burma
 Terrane. Furthermore, our diversification analyses show no diversification
 rate changes through time and across geographic space in this family, but
 the genus Althepus displays an accelerated rate of species diversification
 driven by the remarkable expansion of leg length. Trait evolution analysis
 shows that ecological trait divergence contributes to the diversification
 and accumulation of tropical spiders by facilitating species coexistence.
 These findings provide empirical evidence that the ecological trait
 divergence over evolutionary time scales is key to forming species
 diversity hotspots in SE Asia. Thus, this study integrating molecular
 evidence and paleontological interpretation provides a new framework for
 understanding the evolution of tropical species diversity.
description: DNA alignments (iqtree.zip): the dataset contains 202 extant psilodercid
 species sequenced with the previous seven classical markers (Table S2)
 20221101final5c_need.phy 20221101final16s_need.phy
 20221101final18s_need.phy 20221101final28s_need.phy
 20221101finalco1_need.phy 20221101finalh3_need.phy
 20221101finalwnt_need.phy morphological alignments (iqtree.zip)
 morph1101.phy concatenated alignment: alignments of the molecular data;
 the dataset contains morphological and molecular data (Table S1 and S2)
 20221101finallox.phy (molecular_data.zip) 20221101finallox.nex
 (molecular_data.zip) psi_TE0103.nex (iqtree.zip) phylogenetic trees
 20221101finallox.nex.con.tre (molecular_data.zip)
 RAxML_bipartitions.20221101finallox.tre (molecular_data.zip)
 psi_TE0103.nex.contree (iqtree.zip) Divergence Time Analyses and Marginal
 likelihood estimation using path sampling and stepping-stone sampling in
 BEAST 1.10.4. 20221101finallox3_bd1.xml (molecular_data.zip)
 20221101finallox3_y1.xml (molecular_data.zip)
 20221101finallox_y3_3.xml (molecular_data.zip) dated trees
 20221101finallox3_yall.trees.out.tre (molecular_data.zip) species
 distribution psilodercinae_removeroot_fossil_burma_9 (molecular_data.zip)
 R scripts and codes scripts (scripts.zip)
DOI: 10.5061/dryad.cnp5hqc8v
title: Data from: A meta-analysis of plant tissue O2 dynamics

description: This dataset includes 1,567 recorded tissue O2 levels from 112 plant
 species extracted from published literature. The data forms the basis of
 the publication "A meta-analysis of plant tissue O2 dynamics"
 with the following abstract:Adequate tissue O2 supply is crucial for plant
 functioning. We therefore aimed at identifying environmental conditions
 and plant characteristics affecting plant tissue O2 status. We extracted
 data and performed meta-analysis on &gt; 1,500 published tissue O2
 measurements from 112 species. Tissue O2 status ranged from anoxic
 conditions in especially roots, to &gt; 53 kPa in submerged,
 photosynthesizing shoots. Using information-theoretic model selection, we
 identified ‘submergence’, ‘light’, ‘tissue type’ as well as ‘light ×
 submergence’ interaction as significant drivers of tissue O2 status.
 Median O2 status was especially low (&lt; 50% of atmospheric
 equilibrium) in belowground rhizomes, potato tubers and root nodules. Mean
 shoot and root O2 was ~25% higher in light than in dark when shoots had
 atmospheric contact. However, light showed a significant interaction with
 submergence on plant O2, with a submergence-induced 44% increase in light,
 compared with a 42% decline in dark, relative to plants with atmospheric
 contact. During submergence, ambient water column O2 and shoot tissue O2
 correlated stronger in darkness than in light conditions. Although
 miniaturised Clark-type O2 electrodes in particular have resulted in
 enhanced understanding of plant O2 dynamics, the use of non-invasive
 methods is still lacking behind its widespread use in mammalian tissues.
description: We performed a structured and
 systematic literature search to identify studies reporting
 O<sub>2</sub> measurements in vegetative plant tissues. The
 search was conducted using the Web of Science BIOSIS database applying
 Boolean operators, as explained in detail in the Supplementary Materials.
 The search resulted in a final list of 129 studies published up until
 September 2022. We
 extracted each observation of plant tissue O<sub>2</sub> status and entered it into a database alongside
 information of plant species, tissue type, light conditions, submergence
 status, treatment, O<sub>2</sub> measurement technique, tissue excisions status,
 etc. if provided in the source. The studies used for this review provide a wide
 range of ways to measure and report levels of plant tissue
 O<sub>2</sub>. Details on data extractions, unit conversions,
 etc. are available in the related publication. Data were extracted from
 publication text, tables or graphs using ImageJ. Please also see the
 accompanied README file for additional information on data structure
 etc.<br>
DOI: 10.5061/dryad.b5mkkwhhv
title: Clay lick usage by wild mixed-species parrot groups at the Colpa Colorado from Oct through Dec 2002–2012

description: This data was collected at the Colpa Colorado, a clay lick in southeastern
 Peru (13° 080' S, 69° 370' W), as part of a long-term
 monitoring project conducted by The Macaw Society (formerly known as the
 Tambopata Macaw Project). This data set documents the clay lick visitation
 rates of 12 species of parrots during the early wet season (Oct-Dec) from
 2002-2012. Field assistants recorded the number of individuals of each
 species present on several pre-defined zones of the clay lick at regular
 5-minute intervals, starting with the time when the first parrot lands on
 the clay lick in the morning. The vast majority of clay lick usage occurs
 in the early morning and this release contains data up until 9 am every
 day. This data set is unique for its longitudinal nature (spanning 11
 years), fine-grained temporal resolution (with scans conducted every 5
 minutes), and spatial resolution (with parrot numbers recorded for 11
 standardized zones per scan).
DOI: 10.5061/dryad.2v6wwpzt7
title: Data from: Fungal symbionts generate water-saver and water-spender plant drought strategies via diverse effects on host gene expression

description: Panicum hallii var hallii HAL2 plants were
 inoculated individually with six foliar fungal endophytes or fungus-free
 controls and subjected to 5% or 20% soil moisture treatments. The fungi
 were selected for their previously observed effects on plant drought
 physiology, inducing either a “water saver” or a “water spender” strategy
 in the host. Plants were grown in enclosed microcosms to prevent
 cross-contamination and each treatment and control included 6 replicates.
 All fungi were Ascomycetes isolated from plants in central Texas. Plants
 were monitored for height, wilt, water loss, and survival. At the harvest,
 we also measured biomass and leaf colonization by the fungi and
 flash-froze leaf tissue for transcriptomic analyses. Both plant response
 and gene expression data are provided.
description: Plants were grown in microcosms with fungal inocula or
 fungus-free controls, under drought (5% gravimetric) or well-watered (20%
 gravimetric) soil moisture. Every 3 days, plants were measured for height,
 wilt resistance (days to first wilt), and survival (days to first tiller
 death). Microcosms were also weighed for whole-plant water loss, and water
 was added as needed to maintain treatments. Relative height growth rate
 (RGR) and water loss rate were calculated from the repeated measurements
 as the change over time. After application of the water treatments for 21
 days, three replicates were used to measure fungal leaf colonization
 rates. The remaining three replicates from each treatment were harvested
 for RNAseq by flash-freezing in liquid N2 immediately after measuring
 fresh weight.  Read number and quality of the RNA-seq
 libraries were determined with FastQC. To analyze the RNA-seq libraries,
 reads of each sample were mapped to the <em>Panicum</em>
 <em>hallii</em> var <em>hallii</em> HAL2 genotype
 v2.1 reference genome available through the DOE Joint Genome Institute
 (http://phytozome.jgi.doe.gov/) with TuxNet using default settings. TuxNet uses ea-utils fastq-mcf for Illumina read processing, hisat2 for alignment, and Cufflinks for differential expression analysis. Sequence data are available at the NCBI Sequence Read Archive (PRJNA777108).
DOI: 10.5061/dryad.7h44j0zzs
title: Large leaf hydraulic safety margins limit the risk of drought-induced leaf hydraulic dysfunction in Neotropical rainforest canopy tree species

description: The sequence of key water potential thresholds from the onset of water
 stress to mortality, and the timing of stomatal closure with regard to
 leaf xylem embolism formation are essential to characterizing plant
 adaptive strategies to drought. This constitutes a critical knowledge gap
 for tropical rainforest species, which may be less vulnerable to drought
 than previously thought. We recorded key leaf and stem water potential
 thresholds, leaf hydraulic safety margins (HSMleaf), leaf stomatal safety
 margins (SSMleaf) and estimated native embolism levels during a
 normal-intensity dry season across 18 Neotropical rainforest tree species.
 We also solved a sequence of key water potential thresholds. Additionally,
 we provide a cross-biome analysis of SSMleaf encompassing 97 species from
 four major biomes based on a literature survey. In the studied rainforest
 species, leaf turgor loss point, used as a surrogate for stomatal closure,
 typically occurred before the onset of leaf xylem embolism. Most species
 exhibited positive HSMleaf and SSMleaf, with contrasting values across
 species and nearly absent embolism levels during the dry season
 irrespective of the experienced midday leaf water potentials. Our results
 point out that leaf xylem embolism is not routine for Neotropical
 rainforest tree species. Based on our proposal of the water potential
 sequence for tropical rainforest trees, we argue that leaf xylem embolism
 is a rare event for these species. This was supported by the literature
 survey, indicating that across biomes, most woody species have rather
 large SSMleaf and that leaves of tropical rainforest trees are not
 necessarily more vulnerable than in other biomes. However, we found
 evidence that some tropical rainforest species may be more vulnerable than
 others to ongoing climate change. Our data provide an opportunity to
 parametrize tree-based or land-surface models for tropical rainforests.
DOI: 10.5061/dryad.83bk3j9wg
title: Carbon-biodiversity relationships in a highly diverse subtropical forest

description: Carbon-focused climate mitigation strategies are becoming increasingly
 important in forests. However, with ongoing biodiversity declines, we
 require better knowledge of how much such strategies account for
 biodiversity. We particularly lack information across multiple trophic
 levels and on established forests, where the interplay between carbon
 stocks, stand age and tree diversity might influence carbon–biodiversity
 relationships. Using a large dataset (&gt;4,000 heterotrophic species
 of 23 taxonomic groups) from secondary, subtropical forests, we tested how
 multitrophic diversity and diversity within trophic groups relate to
 aboveground, belowground, and total carbon stocks at different levels of
 tree species richness and stand age. Our study revealed that aboveground
 carbon, the key component of climate-based management, was largely
 unrelated to multitrophic diversity. By contrast, total carbon stocks—i.e.
 including belowground carbon—emerged as a significant predictor of
 multitrophic diversity. Relationships were non-linear and strongest for
 lower trophic levels, but non-significant for higher trophic level
 diversity. Tree species richness and stand age moderated these
 relationships, suggesting long-term regeneration of forests may be
 particularly effective in reconciling carbon and biodiversity targets. Our
 findings highlight that the biodiversity benefits of climate-oriented
 management need to be evaluated carefully, and only maximizing aboveground
 carbon may fail to account for biodiversity conservation requirements.
description: Full details on measurements
 and estimation methods for all carbon components are provided in Liu et
 al. (2018). We used tree
 species richness and woody plant diversity as key predictors of
 heterotrophic biodiversity and carbon stocks. Woody plant diversity was
 completely inventoried in 2008 quantified as the number of tree and shrub
 species &gt; 1 m height per plot. We assessed heterotrophic biodiversity for seven
 groups of organisms that aggregated data for a total of 23 taxa of
 aboveground arthropods, soil fungi, and bacteria. The
 sampling of heterotrophs
 was conducted between 2008 and 2012 with a set of methods that cover the
 wide range of habitat use and activity patterns of arthropods and
 microorganisms and that were best suited to assess the focal taxa.
 Further information is
 provided in Schuldt et al. (2015) <em>Nature
 Communications</em>. Carbon stocks were quantified for aboveground,
 forest-floor, and belowground carbon in Mg C ha-<sup>1</sup>.
 Full details on
 measurements and estimation methods for all carbon components are provided
 in Liu et al. (2018) <em>Proceedings B</em>.
DOI: 10.5061/dryad.cvdncjt7x
title: Data from: Multi-level thresholds of residential and agricultural land use for elk avoidance across the Greater Yellowstone Ecosystem

description: 1. Conversion of land for settlements and agriculture is increasing
 globally and can influence wildlife space use. However, there is limited
 research to identify the thresholds of land use change that incur wildlife
 avoidance, and how these thresholds might vary across levels of selection.
 2. We evaluated multi-level avoidance thresholds of elk (Cervus
 canadensis) impacted by residential development and irrigated agriculture
 across the Greater Yellowstone Ecosystem in Idaho, Montana, and Wyoming.
 Using GPS data from 765 elk in 21 herds, we estimated habitat selection in
 relation to development and agriculture at 3 levels (home range selection,
 within home range selection, and movement path selection). Next, using
 individual selection covariates and associated measures of land use
 availability, we used functional-response models to evaluate how selection
 varied based on availability, and in turn, to estimate avoidance
 thresholds. 3. We found individual and level-specific variation in elk
 responses to environmental factors. Elk exhibited stronger responses
 (either selection or avoidance) when selecting home range locations (i.e.
 second-order selection) than when selecting areas within home ranges (i.e.
 third-order selection) or selecting movement paths (i.e. fourth order
 selection). Importantly, elk avoidance of development and agriculture
 changed as the amount of land in these categories changed. Across all
 levels of selection, elk exhibited neutral selection for human development
 at low levels of availability (&lt;1.1–2.2% developed) but avoided
 areas that were &gt;1.1–2.2% developed. Conversely, elk selected
 positively for irrigated agriculture at low to moderate levels of
 availability (&lt;52.0–66.2% agriculture) but exhibited neutral
 selection in areas that were &gt; 52.0–66.2% agriculture. 4. Synthesis
 and Applications: Elk avoidance of low levels of human development
 suggests conservation efforts such as restrictions on future development
 or conservation easements could focus on areas that are still below 2%
 developed. Additionally, because elk selection was strongest at the
 landscape scale, conservation actions that are based on information about
 the overall landscape structure may be most impactful. Our results
 highlight the importance of understanding variability in wildlife habitat
 selection at multiple levels, particularly in relation to land use change
 and highlight how functional response modelling can help inform landscape
 conservation.
DOI: 10.5061/dryad.2z34tmpr6
title: Data for: Natural genetic variation in a dopamine receptor is associated with variation in female fertility in Drosophila melanogaster

description: Fertility is a major component of fitness but its genetic architecture
 remains poorly understood. Using a full diallel cross of
 50 Drosophila melanogaster Genetic Reference Panel
 inbred lines with whole genome sequences, we found substantial genetic
 variation in fertility largely attributable to females. We mapped genes
 associated with variation in female fertility by genome-wide association
 analysis of common variants in the fly genome. Validation of candidate
 genes by RNAi knockdown confirmed the role of the dopamine 2-like receptor
 (Dop2R) in promoting egg laying. We replicated
 the Dop2R effect in an independently collected
 productivity dataset and showed that the effect of
 the Dop2R variant was mediated in part by regulatory
 gene expression variation. This study demonstrates the strong potential of
 genome-wide association analysis in this diverse panel of inbred strains
 and subsequent functional analyses for understanding the genetic
 architecture of fitness traits.
description: Please refer to https://github.com/qgg-lab/dgrp-diallel for computer codes.
DOI: 10.5061/dryad.wwpzgmspq
title: Data for: Morphological covariance and onset of foot prehensility as indicators of integrated evolutionary dynamics in the herons (Ardeidae)

description: The ultimate form an organism attains is based, in part, on the rate and
 timing of developmental trajectories and on compensatory relationships
 between morphological traits. For example, there is often an inverse
 correlation between the relative size of an organism’s head and the length
 of its legs. Avian examples with disproportionately small heads and long
 legs include ostriches (Struthionidae), flamingos (Phoenicopteridae),
 cranes (Gruidae), stilts (Recurvirostridae), and storks (Ciconiidae). To
 determine whether a possible compensatory relationship exists between
 relative head size and hind-limb length in a typically long-legged family
 of birds—the Ardeidae—we measured skull dimensions (length, width, and
 height of cranium, and total skull length, including culmen) and skeletal
 hind-limb dimensions (femur, tibiotarsus, and tarsometatarsus) of the 12
 North American species (north of Mexico) and of 12 additional taxa,
 including the morphologically divergent Agamia and Cochlearius. Our
 analyses reveal a negative allometric relationship between head size and
 leg length. For example, Ardea species exhibit the smallest relative head
 sizes and the longest legs, while Butorides, Nycticorax, Nyctanassa, and
 Cochlearius have among the largest heads relative to hind-limb length.
 Furthermore, both positive and negative allometries occur in paired
 comparisons between the three hind-limb bones, resulting in tall
 morphotypes having disproportionately short femurs while small morphotypes
 exhibit long femurs; this relationship has implications for foraging
 behavior. Moreover, long legs of Ardea apparently derive from an extended
 growth period, or hypermorphosis, while relatively short legs of Butorides
 result from growth truncation. The latter are thus morphologically
 paedomorphic features that, paradoxically, permit a functional
 precociality of the hind limbs: early onset of prehensile ability of the
 feet for grasping branches, which nestlings retain into adulthood, later
 expressed in foraging mode. This developmentally accelerated prehensile
 function in small species may be attributed, in part, to selection for
 predator avoidance in the early nestling stage.
DOI: 10.5061/dryad.vhhmgqnzr
title: Data from: Policing is more effective against eggs of non-natal versus natal workers at early colony stages in a bumblebee

description: Eusocial insect colonies are vulnerable to exploitation by egg-laying
 workers arising either as natal reproductive workers or as non-natal
 reproductive 'drifting' workers (intraspecific social
 parasites). Worker egg-laying is potentially costly to the colony, but
 queens and workers can counter its costs via egg-eating (queen or worker
 policing). Bumblebee colonies exhibit egg laying by both natal and
 non-natal workers: natal workers collectively lay more eggs but do so only
 after a specific point in the colony cycle, the ‘competition point’,
 whereas non-natal workers potentially lay eggs throughout the colony
 cycle. These features create a special opportunity to investigate whether
 policing of worker-laid eggs is context-dependent (i.e. depends on worker
 origin of eggs and/or colony stage). We introduced artificial egg cells
 containing eggs laid by either natal or non-natal workers into colonies of
 the bumblebee Bombus terrestris both before and after their competition
 points, and observed the fate of introduced egg cells and eggs. In both
 colony stages, the majority of introduced egg cells and eggs were policed,
 demonstrating that policing was not activated only after the competition
 point. However, in the pre-competition point stage alone, a smaller
 proportion of non-natal workers' eggs (15%) remained after 20 h
 compared to the proportion of natal workers' eggs remaining (24%).
 More effective policing of non-natal workers' eggs early in the
 colony cycle potentially represents an adaptive, context-dependent
 response to the stage in the cycle when all worker-laid eggs are normally
 unrelated to the natal colony.
DOI: 10.15468/dl.pxkmmy
title: Occurrence Download

description: A dataset containing 1661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-156.93294 16.31271,-65.17308 16.31271,-65.17308 53.03746,-156.93294 53.03746,-156.93294 16.31271))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pheidole moerens Wheeler, 1908"
 ]
}

 The dataset includes 1661 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064153-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d2nbc9
title: Occurrence Download

description: A dataset containing 1027 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tetramorium lanuginosum Mayr, 1870"
 ]
}

 The dataset includes 1027 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064155-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.