cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qz612jmgm
title: Data from: Arbuscular mycorrhizal fungi communities shaped by host-plant affect the outcome of plant-soil feedback in dryland restoration

description: 1. Plant inoculation with Arbuscular mycorrhizal fungi (AMF) can be a
 useful tool to overcome challenges in dry forest restoration. However,
 advances are still needed to guide choices regarding soil origin and
 inoculum production methods, since outcomes can vary due to plant-soil
 feedbacks (PSF). We evaluate how soil origin and host plant used for
 inoculum production affect AMF community and therefore the plant biomass
 accumulation and functional traits. 2. In the conditioning phase, we
 investigated whether soils originating from a recovered area (Quarry) and
 a vegetation fragment (Caatinga) would have their AMF communities modified
 due to the growth of Sorghum bicolor (used for inoculum production) and
 Senna uniflora (used in Brazilian semiarid restoration). In the feedback
 phase, we compared the performance of four plants species growing on a
 degraded soil and inoculated or not by a mixture of AMF isolates in
 comparison to soil inoculum prepared from the conditioning phase. 3. The
 inoculum from Caatinga presented seven times more AMF species compared to
 that from the Quarry, which presented ruderal and stress tolerant species.
 The soil inoculum conditioned by S. uniflora, regardless of origin,
 presented greater evenness compared to the soil inoculum produced with S.
 bicolor and promoted 33% more plant biomass compared to the control
 without inoculation. Root colonization by AMF increased PSF and decreased
 plant investment in functional traits such as specific root length (SRL)
 and specific leaf area (SLA). 4. Our results demonstrate the importance of
 adopting strategies that preserve local adaptation of inoculants produced.
 The use of native plant for propagation of native AMF in the conditioning
 phase provided more positive responses for Mesosphaerum suaveolens and
 Rhaphiodon echinus than inoculated with introduced AMF isolates. This is
 probably due to the interaction of inoculated plants with responsive AMF
 present in the soil. 5. Synthesis and applications: Our study shows that
 conditioning field-collected soil with S. uniflora and using it for
 inoculation can be a simple technique to promote biomass accumulation for
 other native herbaceous species. This preserves the compatibility between
 the soil inoculum produced with native AMF and native plants, representing
 an important tool for restoration programs.
DOI: 10.5061/dryad.tmpg4f50h
title: Data and R code for: Temperature-induced multispecies cohort effects in sympatric snakes

description: In reptiles, reproductive maturity is often determined by size rather than
 age. Consequently, growth early in life may influence population dynamics
 through effects on generation time and survival to reproduction. Because
 reproductive phenology and pre- and post-natal growth are
 temperature-dependent, environmental conditions may induce multi-species
 cohort effects on body size in sympatric reptiles. I present evidence of
 this using ten years of neonatal size data for three sympatric viviparous
 snakes, Dekay’s Brownsnakes (Storeria dekayi), Red-bellied Snakes (S.
 occipitomaculata) and Common Gartersnakes (Thamnophis sirtalis).
 End-of-season neonatal size varied in parallel across species such that
 snout-vent length was 36-61% greater and mass was 65-223% greater in years
 when gestating females could achieve higher April-May (vs. June-July or
 August-September) operative temperatures. Thus, temperature had a larger
 impact during follicular enlargement and ovulation than during gestation
 or post-natal growth. Multi-species cohort effects like these may affect
 population dynamics and increase with climate change.
DOI: 10.5061/dryad.qv9s4mwfv
title: Data from: Simulating climate change in situ in a tropical rainforest understorey using active air warming and CO2 addition

description: Background: Future climate-change effects on plant growth are most
 effectively studied using microclimate-manipulation experiments, the
 design of which has seen much advance in recent years. For tropical
 forests, however, such experiments are particularly hard to install and
 have hence not been widely used. We present a system of active heating and
 CO2 fertilisation for use in tropical forest understoreys, where passive
 heating is not possible. The system was run for two years to study
 climate-change effects on epiphytic bryophytes, but is also deemed
 suitable to study other understorey plants. Methods: Warm-air and CO2
 addition were applied in 1.6-m tall, 1.2-m diameter hexagonal open-top
 chambers and the microclimate in the chambers compared to outside air.
 Warming was regulated with a feedback system while CO2 addition was fixed.
 Results: The setup successfully heated the air by 2.8K and increased CO2
 by 250 ppm, on average, with +3K and +300 ppm as the targets. Variation
 was high, especially due to technical break-downs, but not biased to times
 of the day or year. In the warming treatment, absolute humidity slightly
 increased but relative humidity dropped by between 6 to 15% (and the
 vapour-pressure deficit increased) compared to ambient, depending on the
 level of warming achieved in each chamber. Conclusions: Compared to other
 heating systems, the chambers provide a realistic warming and CO2
 treatment, but moistening the incoming air would be needed to avoid drying
 as a confounding factor. The method is preferable over infrared heating in
 the radiation-poor forest understory, particularly when combined with CO2
 fertilisation. It is suitable for plant-level studies, but ecosystem-level
 studies in forests may require chamber-less approaches like infrared
 heating and free-air CO2 enrichment. By presenting the advantages and
 limitations of our approach we aim to facilitate further climate-change
 experiments in tropical forests, which are urgently needed to understand
 the processes determining future element fluxes and biodiversity changes
 in these ecosystems.
description: We here present the microclimatic data used in this paper. The
 list of data files together with their detailed explanations can be found
 in the README.pdf
DOI: 10.15468/dl.pfbtav
title: Occurrence Download

description: A dataset containing 21353 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Aspergillus clavatus, Aspergillus oryzae, Byssochlamys nivea, Claviceps purpurea, Claviceps fusiformis, Claviceps africana, Paecilomyces niveus)"
 ]
}

 The dataset includes 21353 records from 345 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002966-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c2fqz6191
title: Data from: Exploring conflicts in whole genome phylogenetics: A case study within Manakins (Aves: Pipridae)

description: Some phylogenetic problems remain unresolved even when large amounts of
 sequence data are analyzed and methods that accommodate processes such as
 incomplete lineage sorting are employed. In addition to investigating
 biological sources of phylogenetic incongruence, it is also important to
 reduce noise in the phylogenomic dataset by using an appropriate filtering
 approach that addresses gene tree estimation errors. We present the
 results of a case study in manakins, focusing on the very difficult clade
 comprising the genera Antilophia and Chiroxiphia. Previous studies suggest
 that Antilophia is nested within Chiroxiphia, though relationships among
 Antilophia+Chiroxiphia species have been highly unstable. We extracted
 more than 11,000 loci (ultra-conserved elements and introns) from whole
 genomes and conducted analyses using concatenation and multi-species
 coalescent methods. Topologies resulting from analyses using all loci
 differed depending on the data type and analytical method, with two clades
 (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin
 tree showing incongruent results. We hypothesized that gene trees that
 conflicted with a long coalescent branch (e.g., the branch uniting
 Antilophia+Chiroxiphia) might be enriched for cases of gene tree
 estimation error, so we conducted analyses that either constrained those
 gene trees to include monophyly of Antilophia+Chiroxiphia or excluded
 these loci. While constraining trees reduced some incongruence, excluding
 the trees led to completely congruent species trees, regardless of the
 data type or model of sequence evolution used. We found that a suite of
 gene metrics (most importantly the number of informative sites and
 likelihood of intralocus recombination) collectively explained the loci
 that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found
 evidence for introgression that may have contributed to the discordant
 topologies we observe in Antilophia+Chiroxiphia and led to deviations from
 expectations given the multi-species coalescent model. Our study
 highlights the importance of identifying factors that can obscure
 phylogenetic signal when dealing with recalcitrant phylogenetic problems,
 such as gene tree estimation error, incomplete lineage sorting and
 reticulation events.
DOI: 10.5061/dryad.08kprr53h
title: Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie

description: Diet analysis integrates a wide variety of visual, chemical and biological
 identification of prey.  Samples are often treated as
 compositional data, where each prey is analyzed as a continuous percentage
 of the total.  However, analyzing compositional data results in
 analytical challenges, e.g., highly parameterized models or prior
 transformation of data.  Here, we present a novel approximation
 involving a Tweedie generalized linear model (GLM).  We first
 review how this approximation emerges from considering predator foraging
 as a thinned and marked point process (with marks representing prey
 species and individual prey size).  This derivation can motivate
 future theoretical and applied developments.  We then provide a
 practical tutorial for the Tweedie GLM using new package mvtweedie that
 extends capabilities of widely used packages in R (mgcv and ggplot2) by
 transforming output to calculate prey compositions.  We
 demonstrate this approach and software using two examples. Tufted puffins
 (Fratercula cirrhata) provisioning their chicks on a colony in the
 northern Gulf of Alaska show decadal prey switching among sand lance and
 prowfish (1980-2000) and then Pacific herring and capelin (2000-2020),
 while wolves (Canis lupus ligoni) in Southeast Alaska forage on mountain
 goats and marmots in northern uplands and marine mammals in seaward island
 coastlines. 
description: File
 list  Reproducible_script_R1.R
 Wolf.csv Seabird.csv
 MDO.seabirdforagingarea.SST.csv
 <b>Description</b>
 Reproducible_script_R1.R – R script used to replicate all
 analysis and figures in main text and appendices.  See comments at top for
 directions prior to running.  Wolf.csv -  CSV file
 containing four columns used in the wolf metabarcoding case-study in Fig.
 3 of the main text: “Latitude” -- Latitude
 of scat sample in Degree-decimals; “Longitude” --
 Longitude of scat sample; “group” -- prey taxonomic
 group used in analysis; “Response” -- metabarcoding
 read count used as response variable. 
 Seabird.csv -  CSV file containing three columns used in the
 seabird bill-load case-study in Fig. 2 of the main text:
 “Year” – Year AD for bill-load sample;
 “group” -- prey taxonomic group used in analysis;
 “Response” – bill-load count used as response
 variable. MDO.seabirdforagingarea.SST.csv
 -  CSV file containing two additional columns used in the seabird
 bill-load case-study in Fig. 2 of the main text: 
 “Year” – Year AD, including all Years used in Fig. 2;
 “SST_mean” – average sea surface temperature near Middleton
 Island;
DOI: 10.5061/dryad.7m0cfxpvv
title: Data from: The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection

description: Emerging epidemics and local infection clusters are initially prone to
 stochastic effects that can substantially impact the epidemic trajectory.
 While numerous studies are devoted to the deterministic regime of an
 established epidemic, mathematical descriptions of the initial phase of
 epidemic growth are comparatively rarer. Here, we review existing
 mathematical results on the epidemic size over time, and derive new
 results to elucidate the early dynamics of an infection cluster started by
 a single infected individual. We show that the initial growth of epidemics
 that eventually take off is accelerated by stochasticity. These results
 are critical to improve early cluster detection and control. As an
 application, we compute the distribution of the first detection time of an
 infected individual in an infection cluster depending on the testing
 effort, and estimate that the SARS-CoV-2 variant of concern Alpha detected
 in September 2020 first appeared in the United Kingdom early August 2020.
 We also compute a minimal testing frequency to detect clusters before they
 exceed a given threshold size. These results improve our theoretical
 understanding of early epidemics and will be useful for the study and
 control of local infectious disease clusters.
description: Codes and datasets for generating the figures in the main text
 and the Supplementary Information of the manuscript entitled "The
 stochastic dynamics of early epidemics: probability of establishment,
 initial growth rate, and infection cluster size at first detection"
 published in the Journal of the Royal Society Interface.
DOI: 10.5061/dryad.ghx3ffbq7
title: Domain organization of lentiviral and betaretroviral surface envelope glycoproteins modeled with AlphaFold

description: The surface envelope glycoproteins of non-primate lentiviruses and
 betaretroviruses share sequence similarity with the inner proximal
 domain  b-sandwich of the human immunodeficiency virus
 type 1 (HIV-1) gp120 glycoprotein that faces the transmembrane
 glycoprotein as well as patterns of cysteine and glycosylation site
 distribution that points to a similar two-domain organization in at least
 some lentiviruses. Here, high reliability models of the surface
 glycoproteins obtained with the AlphaFold algorithm are presented for the
 gp135 glycoprotein of the small ruminant caprine arthritis-encephalitis
 (CAEV) and visna lentiviruses and the betaretroviruses jaagsiekte sheep
 retrovirus (JSRV), mouse mammary tumor virus (MMTV) and consensus human
 endogenous retrovirus type K (HERV-K). The models confirm and extend the
 inner domain structural conservation in these viruses and identify two
 outer domains with a putative receptor binding site in the CAEV and visna
 virus gp135. The location of that site is consistent with patterns of
 sequence conservation and glycosylation site distribution in gp135. In
 contrast, a single domain is modeled for the JSRV, MMTV and HERV-K
 betaretrovirus envelope proteins that is highly conserved structurally in
 the proximal region and structurally diverse in apical regions likely to
 interact with cell receptors. The models presented here identify sites in
 small ruminant lentivirus and betaretrovirus envelope glycoproteins likely
 to be critical for virus entry and virus neutralization by antibodies and
 will facilitate their functional and structural characterization.
description: The mature region of the surface envelope glycoproteins of
 non-primate lentiviruses and betaretroviruses were modeled using a
 simplified AlphaFold 2 method without templates, accessible with graphics
 processing unit support through the Colab server at
 https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb. GenBank accession number for the sequences used in modeling of CAEV-CO, CAEV-63, visna virus KV1772 gp135 and visna virus K1514 gp135 and FIV, EIAV, BIV and JDV, MMTV and JSRV surface envelope glycoproteins are M60855, L06906, U21603, X01811 and M80216.
description: B-factors column (column 11) indicate pLDDT reliability scores
 for structural predictions.
DOI: 10.5061/dryad.s4mw6m97d
title: Spatiotemporal evolution of the global species diversity of Rhododendron

description: Evolutionary radiation is a widely recognized mode of species
 diversification, but its underlying mechanisms have not been unambiguously
 resolved for species-rich cosmopolitan plant genera. In particular, it
 remains largely unknown how biological and environmental factors have
 jointly driven its occurrence in specific regions. Here we use
 Rhododendron, the largest genus of woody plants in the Northern
 Hemisphere, to investigate how geographic and climatic factors, as well as
 functional traits, worked together to trigger plant evolutionary
 radiations and shape the global patterns of species richness based on a
 solid species phylogeny. Using 3437 orthologous nuclear genes, we
 reconstructed the first highly supported and dated backbone phylogeny of
 Rhododendron comprising 200 species that represent all subgenera,
 sections, and nearly all multi-species subsections, and found that most
 extant species originated by evolutionary radiations when the genus
 migrated southwards from circumboreal areas to tropical/subtropical
 mountains, showing rapid increases of both net diversification rate and
 evolutionary rate of environmental factors in the Miocene. We also found
 that the geographically uneven diversification of Rhododendron led to a
 much higher diversity in Asia than in other continents, which was mainly
 driven by two environmental variables, i.e., elevation range and annual
 precipitation, and was further strengthened by the adaptation of leaf
 functional traits. Our study provides a good example of integrating
 phylogenomic and ecological analyses in deciphering the mechanisms of
 plant evolutionary radiations and sheds new light on how the
 intensification of the Asian monsoon has driven evolutionary radiations in
 large plant genera of the Himalaya-Hengduan Mountains.
description: We sampled a total of 202 species of
 <em>Rhododendron</em> for transcriptome sequencing<em>.
 </em>Those<em> </em>paired-end reads of 100 bp or 150 bp
 used in <em>de novo</em> assembly with Trinity v. 2.0.6. After
 discarding redundant transcripts using CD-HIT v. 4.6.5 with a similarity
 threshold of 1, the longest transcript of each gene was retained. The
 coding sequences (CDS) were identified with TransDecoder v. 0.36, and the
 CDS encoding the longest peptide was retained for the ortholog search. We
 used 3437 OGs  in phylogenetic reconstruction with the maximum-likelihood
 (ML) method in IQ-TREE v.2.0-rc1. We used RelTime method and MCMCTree
 program in divergence time estimation. Ancestral areas were reconstructed
 using BioGeoBEARS v.1.1.1 implemented in R v.3.6.2. The diversification
 rates and major shifts were evaluated by BAMM. RPANDA was further used to
 investigate the impact of global paleo-temperature on the diversification
 of <em>Rhododendron </em>based on nine temperature-dependent
 likelihood models.
DOI: 10.5061/dryad.pzgmsbcnd
title: Long term irrigation experiment

description: Climate change exposes ecosystems to strong and rapid changes in their
 environmental boundary conditions mainly due to the altered temperature
 and precipitation patterns. It is still poorly understood how fast
 interlinked ecosystem processes respond to altered environmental
 conditions, if these responses occur gradually or suddenly when thresholds
 are exceeded, and if the patterns of the responses will reach a stable
 state. We conducted an irrigation experiment in the Pfynwald, Switzerland
 from 2003-2018. A naturally dry Scots pine (Pinus sylvestris L.) forest
 was irrigated with amounts that doubled natural precipitation, thus
 releasing the forest stand from water limitation. The aim of this study
 was to provide a quantitative understanding on how different traits and
 functions of individual trees and the whole ecosystem responded to
 increased water availability, and how the patterns and magnitudes of these
 responses developed over time. We found that the response magnitude, the
 temporal trajectory of responses, and the length of initial lag period
 prior to significant response largely varied across traits. We detected
 rapid and stronger responses from above-ground tree traits (e.g.,
 tree-ring width, needle length, and crown transparency) compared to
 below-ground tree traits (e.g., fine root biomass). The altered
 above-ground traits during the initial years of irrigation increased the
 water demand and trees adjusted by increasing root biomass during the
 later years of irrigation, resulting in an increased survival rate of
 Scots pine trees in irrigated plots. The irrigation also stimulated
 ecosystem-level foliar decomposition rate, fungal fruit body biomass, and
 regeneration abundances of broadleaved tree species. However, irrigation
 did not promote the regeneration of Scots pine trees which are reported to
 be vulnerable to extreme droughts. Our results provide extensive evidence
 that tree- and ecosystem-level responses were pervasive across a number of
 traits on long-term temporal scales. However, after reaching a peak, the
 magnitude of these responses either decreased or reached a new stable
 state, providing important insights into how resource alterations could
 change the system functioning and its boundary conditions.
description: The information is provided in the main manuscript.
DOI: 10.5061/dryad.6wwpzgn0p
title: Data from: The extension of foundress lifespan and the evolution of eusociality in the Hymenoptera

description: The evolution of effectively sterile workers in the aculeate Hymenoptera
 (ants, bees and stinging wasps) requires that a female’s lifespan largely
 overlap that of her daughters. The evolution of long nest foundress
 lifespans in eusocial species from the short lifespans of solitary species
 is investigated. Analyses that control for phylogeny show for the first
 time that foundress adult lifespan increases, and first-brood offspring
 development time decreases, with increasing colony size, resulting in the
 ratio of foundress adult lifespan to worker total lifespan increasing with
 increasing colony size. These patterns support the hypothesis that the
 reproductive division of labour increases with increasing colony size,
 explaining the evolution of effectively sterile workers in species with
 large colonies. However, there is a discrete increase in foundress adult
 lifespan in the transition from non-eusociality to eusociality that is
 independent of colony size. An analysis of life history characters
 suggests that this increase is explained by nests being founded by
 multiple females and progressive feeding of larvae as they develop. A
 reduced rate of senescence of a dominant co-foundress may be selected as a
 plastic response to social status if high-risk tasks performed by
 subordinate co-foundresses reduce the dominant’s extrinsic mortality rate.
 Multiple-foundress nests in which one female is responsible for most or
 all the reproduction (semisociality) and in which foundresses are full
 sisters are favoured by haplodiploidy, perhaps explaining why eusociality
 is so common in the Hymenoptera. 
description: Please see publication.