cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pg4f4qrmg
title: A contribution to Gymnosphaera (Cyatheaceae) in mainland Asia: two new species, reinstatement of Cyathea bonii, and their phylogenetic positions

description: Gymnosphaera represents a minor lineage within the scaly
 tree-fern family Cyatheaceae. Tropical and subtropical mainland Asia is a
 main distribution area of Gymnosphaera. However, the species
 diversity of Gymnosphaera is currently incompletely
 known in mainland Asia due to lacking critical revision. Here we present
 new findings of species diversity and their relationships of mainland
 Asian Gymnosphaera based on field surveys, the
 examination of herbarium collections, and phylogenetic analyses of
 sequences of multiple chloroplast and nuclear regions. Two new
 species, G. saxicola from southwestern Yunnan
 and G. bachmaensis from central Vietnam, are
 established. Traditionally recognized G. podophylla is
 revealed to be a complex, from which G. bonii is
 reinstated as a distinct species. Our phylogenetic analyses identified
 four clades within Gymnosphaera in mainland
 Asia: G. denticulata clade, G.
 gigantea clade, G. podophylla clade,
 and G. salletii clade. The new species G.
 saxicola, which is special for its saxicolous habitat, was
 resolved as sister to G. austroyunnanensis in
 the G. salletii clade. The newly discovered G.
 bachmaensis, which is characterized specially by the spathulate frond, was
 positioned in the G. podophylla clade, being sister
 to G. bonii. The mountainous region from south-central Vietnam
 northwards to western Yunnan is a diverse center
 of Gymnosphaera and more species of this group are
 probably to be discovered there.
DOI: 10.5061/dryad.4qrfj6q82
title: Permeability of Neotropical agricultural lands to a key native ungulate – are well-connected forests important?

description: Much of what remains of the Earth’s tropical forests is embedded within
 agricultural landscapes, where forest is reduced and fragmented. As native
 forest ungulates are critical to maintaining forest function, it is
 imperative to understand how this functional group responds to declines in
 forest cover and connectivity resulting from agricultural expansion. We
 addressed this issue by evaluating selection of forest cover and forest
 connectivity by a key native ungulate of Neotropical forests, the
 white-lipped peccary (Tayassu pecari Link 1795, Tayassuidae,
 Cetartiodactyla), in agricultural landscapes of Brazil. We evaluated
 selection using compositional analysis at two hierarchical levels,
 landscape and home range. From 2013 to 2019, we GPS-tracked eight
 white-lipped peccary herds in Southwest Brazil, resulting in a total of
 14,460 GPS locations. We found that herds can live in landscapes with a
 wide range of forest cover (35-81% of home ranges covered by native
 forest), with significant, but not strong, selection at the landscape
 level (p = 0.045). Nevertheless, herds strongly select for forest cover
 within their home ranges (81-97% of locations within native forest; highly
 significant selection at the home-range level: p = 0.008). As for
 connectivity, herds significantly select the largest, most connected
 forest fragments at the landscape level (p=0.04), but not at the
 home-range level (p=0.07). Our results support that Neotropical forests
 within agricultural landscapes need to be well-connected in order to
 preserve this key native ungulate, and maintain long-term forest function.
description: We GPS-tracked
 13 white-lipped peccaries (Tayassu pecari) between 2013 and 2019, in
 farmlands of Southwest Brazil, within the Cerrado biome. We mapped the proportion of
 native forest and how connected the forest was in the Study Areas,
 using  . We tested if white-lipped peccary herds were
 selecting more connected forest compared to what was available, using
 Compositional Analyses.
DOI: 10.5061/dryad.jh9w0vt8v
title: Data from: Plant trait response of tundra shrubs to permafrost and nutrient addition

description: Plants may alter their strategies, such as growth and resource
 acquisition, as a result of climate change, especially in areas like the
 Arctic. These changes might affect in turn ecosystem functions and
 vegetation-climate interactions. Plant traits reflect both strategies and
 plant trade-offs in response to environmental conditions. In combination
 with observational data, experiments mimicking future climate conditions
 and data involving multiple leaf and stem traits, can contribute to a
 better mechanistic understanding of feedbacks between shrub growth
 strategies, permafrost thaw and carbon and energy fluxes. This dataset
 contains both metadata and plant trait data measured in
 individuals of four arctic shrub species under experimental conditions.
 The permafrost thaw and fertilization experiment (Peng et al., 2017) ran
 for four years (2011-2014) in the nature reserve of Kytalyk, north-eastern
 Siberia (70°49'N, 147°28'E). The shrub species, dominant at the
 research site, were the deciduous species Betula nana ssp. exilis
 (Sukazcev) Hultén and Salix pulchra Cham., and the evergreen species Ledum
 palustre ssp. decumbens (Aiton) Hultén and Vaccinium vitis-idaea L.
description: The methods used for generating  and processing the data are
 explained in Iturrate-Garcia et al. (2020);
 https://doi.org/10.5194/bg-2019-498
description: Please read the readme file
 (<em>tundra_shrub_traits_README.txt</em>) for description of
 the data included in the file
 <em>tundra_shrub_traits.csv</em>.
DOI: 10.5061/dryad.00000002b
title: A comparison of tick collection materials and methods in Southeastern Virginia

description: In field studies of tick ecology, observed patterns may be biased by
 sampling methods. Results can vary by species, life stage, and habitat,
 and understanding these biases will improve comparisons of data across
 studies as well as assessment of human disease risk. A direct comparison
 of flagging versus dragging was conducted in southeastern Virginia.
 Transects were surveyed over a six-week period to identify differences in
 species and life stage collected, as well as differences between
 corduroy and denim material and inspection method for drags. Flagging
 collected more Ixodes affinis Neumann (Acari:
 Ixodidae) adults
 and Amblyomma americanum L. (Acari:
 Ixodidae) adults than dragging. Ground inspection was
 more efficient than tree inspection for collection
 of I. affinis adults, with no significant
 difference in inspection method for any other species or life stage.
 Corduroy was found to be more effective than denim in collecting
 nymphal A. americanum, although this may be an
 artifact of three large samples for corduroy collection of these ticks.
 There was no significant difference in Ixodes
 scapularis Say (Acari: Ixodidae) collection in any
 comparison. Dragging, tree inspection, and denim were not found to be more
 efficient in any scenario. This is the first comparison of flagging and
 dragging conducted in the southeastern United States. The community
 composition of ticks in this region greatly differs from regions where
 studies of these commonly used sampling techniques have been conducted. As
 the distributions of ticks continues to change over time, it will be
 important to evaluate best practices annually.
DOI: 10.5061/dryad.nvx0k6dqg
title: Insights from survival analyses during 12 years of anti-VEGF therapy for neovascular age-related macular degeneration

description: Importance: While multiple imputation models for missing data and use of
 mixed effects models generally provide better outcome estimates than using
 only observed data or last observation carried forward in clinical trials,
 such approaches usually cannot be applied to visual outcomes from
 retrospective analyses of clinical practice settings, so-called real-world
 outcomes. Objective: To explore potential utility of survival analysis
 techniques for retrospective clinical practice visual outcomes. Design:
 Retrospective cohort study with 12-year observation period. Setting: A
 tertiary eye center. Participants: Of 10,744 eyes with neovascular AMD
 receiving anti-VEGF therapy between October 2008 and February 2020, 7802
 eyes met study criteria (treatment-naïve, first-treated eyes starting
 anti-VEGF therapy). Main outcome measures: Kaplan-Meier estimates and Cox
 proportional hazards modelling were used to consider: VA reaching ETDRS
 (Early Treatment Diabetic Retinopathy Study) letter score 70 (Snellen
 equivalent 20/40) or better; duration VA sustained at or better than 70
 (20/40); and VA declining to 35 (20/200) or worse. Results: The median
 time to attaining VA letter score ≥ 70 (20/40) was 2.0 years (95% CI 1.87
 - 2.32) after the first anti-VEGF injection. Predictive features were
 baseline VA (HR 1.43 per 5 ETDRS letter score or 1 line [95% CI 1.40 -
 1.46]), baseline age (HR 0.88 per 5 years [95% CI 0.86 - 0.90]), and
 injection number (HR 1.123 [95% CI 1.101 - 1.15]). Of the 56% attaining
 this outcome, median time sustained at 70 (20/40) or better was 1.1 years
 (95% CI 1.1 - 1.2). Conclusions and relevance: Survival analysis
 potentially addresses key limitations of retrospective clinical practice
 (real-world) data by accounting for variable observation time-points and
 follow-up durations. Modelling with multiple covariates reveals factors
 that may help inform the likely visual trajectory of an individual. We
 demonstrate the utility of our proposed analyses by showing that patients
 with neovascular AMD beginning anti-VEGF therapy are more likely to
 experience positive visual outcomes within the first 2.9 years, typically
 maintaining this for 1.1 years, but then deteriorating to poor vision
 within 8.7 years. We believe that this dataset, combined with our
 statistical approach for retrospective analyses, may provide long-term
 prognostic information for patients newly diagnosed with this condition.
DOI: 10.5061/dryad.j9kd51c99
title: Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards

description: Understanding the factors that cause heterogeneity among gene trees can
 increase the accuracy of species trees. Discordant signals across
 the genome are commonly produced by incomplete lineage sorting (ILS) and
 introgression, which in turn can result in reticulate evolution.
 Species tree inference using the multispecies coalescent is designed to
 deal with ILS and is robust to low levels of introgression, but
 extensive introgression violates the fundamental assumption
 that relationships are strictly bifurcating. In this study, we
 explore the phylogenomics of the iconic Liolaemus subgenus of
 South American lizards, a group of over 100 species mostly
 distributed in and around the Andes mountains. Using
 mitochondrial DNA (mtDNA) and genome-wide restriction
 site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred
 a time-calibrated mtDNA gene tree, nDNA species trees, and
 phylogenetic networks. We found high levels of
 discordance between mtDNA and nDNA, which we attribute in part to
 extensive ILS resulting from rapid diversification. These data
 also reveal extensive and deep introgression, which combined with
 rapid diversification, explain the high level of
 phylogenetic discordance. We discuss these findings in the
 context of Andean orogeny and glacial cycles that fragmented, expanded,
 and contracted species distributions. Finally, we use the new
 phylogeny to resolve long-standing taxonomic issues in one of
 the most studied lizard groups in the New World.
DOI: 10.5061/dryad.18931zcvg
title: Data from: A study of bacteria adhesion and microbial corrosion on different stainless steels in environment containing Desulfovibrio vulgaris manuscript

description: Stainless steel is an important material used in many applications due to
 its mechanical strength and corrosion resistant properties. The high
 corrosion resistance of stainless steel is provided by the passive film.
 Different stainless steels have different alloy elements and surface
 properties which could have a significant influence on bacterial
 attachment to the surface and thus might result in different microbial
 corrosion behaviours. In this study, the effect of adhesion of sulphate
 reducing bacteria (SRB) and corrosion behaviour in artificial seawater on
 different stainless steels was investigated. Stainless steel materials
 used were SS 410, SS 420, SS 316 and DSS 2205 and pure chromium. The
 contact angle was measured to study the effect of surface properties of
 materials. Adhesion was measured by counting cells attached to the surface
 of materials. The corrosion behaviour of the materials was measured by
 electrochemical testing including measuring open circuit potential,
 electrochemical impedance spectroscopy and potentiodynamic behaviour. The
 long-term corrosion behaviour of each material was studied after six
 months exposure by measuring weight loss and surface analysis with
 SEM-EDX. The results show the high dependency on hydrophobicity of
 materials surfaces to bacterial attachment. However, bacterial attachment
 did not have a significant effect on the corrosion rate of the materials.
 Pure chromium had the best corrosion resistance to MIC with reduced
 bacterial attachment compared to the stainless steel samples. The nature
 of bacterial attachment and corrosion behaviour of the materials are
 discussed.
description: The data was raw data from experiment.
 Electrochemical test data was process by using Zsimpwin and Echem
 Analysis.
DOI: 10.5061/dryad.x69p8czgh
title: Data from: Optimising sample sizes for animal distribution analysis using tracking data

description: 1. Knowledge of the spatial distribution of populations is fundamental to
 management plans for any species. When tracking data are used to describe
 distributions, it is sometimes assumed that the reported locations of
 individuals delineate the spatial extent of areas used by the target
 population. 2. Here, we examine existing approaches to validate this
 assumption, highlight caveats, and propose a new method for a more
 informative assessment of the number of tracked animals (i.e. sample size)
 necessary to identify distribution patterns. We show how this assessment
 can be achieved by considering the heterogeneous use of habitats by a
 target species using the probabilistic property of a utilisation
 distribution. Our methods are compiled in the R package SDLfilter. 3. We
 illustrate and compare the protocols underlying existing and new methods
 using conceptual models and demonstrate an application of our approach
 using a large satellite tracking data-set of flatback turtles, Natator
 depressus, tagged with accurate Fastloc-GPS tags (n = 69). 4. Our approach
 has applicability for the post-hoc validation of sample sizes required for
 the robust estimation of distribution patterns across a wide range of
 taxa, populations and life history stages of animals.
DOI: 10.5061/dryad.pnvx0k6k3
title: Data from: A circuit mechanism for decision making biases and NMDA receptor hypofunction

description: Decision-making biases can be features of normal behaviour, or deficits
 underlying neuropsychiatric symptoms. We used behavioural psychophysics,
 spiking-circuit modelling and pharmacological manipulations to explore
 decision-making biases during evidence integration. Monkeys showed a
 pro-variance bias (PVB): a preference to choose options with more variable
 evidence. The PVB was also present in a spiking circuit model, revealing a
 potential neural mechanism for this behaviour. To model possible effects
 of NMDA receptor (NMDA-R) antagonism on this behaviour, we simulated the
 effects of NMDA-R hypofunction onto either excitatory or inhibitory
 neurons in the model. These were then tested experimentally using the
 NMDA-R antagonist ketamine, a pharmacological model of schizophrenia.
 Ketamine yielded an increase in subjects' PVB consistent with lowered
 cortical excitation/inhibition balance from NMDA-R hypofunction
 predominantly onto excitatory neurons. These results provide a
 circuit-level mechanism that bridges across explanatory scales, from the
 synaptic to the behavioural, in neuropsychiatric disorders where
 decision-making biases are prominent.
description: This ZIP archive contains the raw data for reproducing the
 analyses in the paper. To access the analysis codes, please see the GitHub
 repository link in the main paper.  The GitHub repository also contains
 a ReadMe file.
DOI: 10.5061/dryad.cz8w9gj1v
title: An experimental test to separate the effects of male age and mating history on female mate choice

description: Should females prefer older males as mates? Male survival to old age might
 indicate the presence of fitness-enhancing genes that increase offspring
 fitness. However, many correlational studies show that mating with older
 males can lower female fecundity, and even reduce offspring fitness due to
 epigenetic or germline mutation effects. One problem in quantifying female
 choice based on male age is that age is usually confounded with mating
 history. This begs a question: Do females choose males based on their age,
 or their mating history? The answer requires an experimental approach, but
 few such studies exist. Here we test if experimentally-induced variation
 in the mating history of old and young males (12 week difference in
 post-maturity age) affects female choice in the eastern mosquitofish
 (Gambusia holbrooki). To vary mating history, adult males were either
 allowed to freely mate with females for three weeks, or they only had
 visual contact with females. Immediately thereafter, we ran four-choice
 mating trials, using association time, to test the effects of male age and
 mating history (2x2 design) on male attractiveness. Females did not show a
 clear preference for males based on either characteristic. This was not
 due to a lack of female choice: females spent significantly more time with
 larger males. In addition, female choice was significantly repeatable
 across four trials: twice as a virgin, twice as a non-virgin. Finally,
 female mating status (virgin or non-virgin) did not affect her choice of
 mate, although virgin females spent significantly more time associating
 with test males.
DOI: 10.5061/dryad.w6m905qn9
title: Data from: Spatiotemporal variation in completeness of the early cynodont fossil record and its implications for mammalian evolutionary history

description: Mammals are the only surviving group of Cynodontia, a synapsid clade that
 first appears in the fossil record in the late Permian, ~260 million years
 ago. Here, using three metrics that capture skeletal completeness, we
 quantify the quality of the early cynodont fossil record in time and space
 to evaluate the impact of sampling and preservational biases on our
 understanding of the group’s evolutionary history. There is no consistent
 global sampling signal for early cynodonts. Completeness of the cynodont
 fossil record increases across the Permian/Triassic boundary, peaking in
 the Early–early Late Triassic. This peak is dominated by specimens from
 southern Africa and South America, where a highly seasonal climate likely
 favoured preservation. Completeness is generally lower thereafter,
 correlated with a shift from a Gondwanan to a predominantly Laurasian
 fossil record. Phylogenetic and stratigraphic congruence in early
 cynodonts is high, although their fossil record exhibits less skeletal
 completeness overall than other tetrapod clades, including the
 contemporaneous anomodont synapsids. This discrepancy could be due to
 differences in the diagnosability of their fossils, especially for
 small-bodied species. Establishing the timing and assembly of derived
 (‘mammalian’) anatomical features in Cynodontia is obscured by sampling.
 Two of the major nodes at which acquisition of mammalian features is
 concentrated (Cynodontia and Mammaliamorpha) suffer from lengthy intervals
 of poor sampling prior to becoming abundant parts of tetrapod faunas. Low
 completeness in these intervals limits our ability to determine when
 certain ‘key’ mammalian characteristics evolved, or to identify the
 selective pressures that might have driven their origins.
description: Please use the latest version of this dataset (December 14,
 2020) Supplementary Data 1 First
 and last appearance dates and locality information for cynodont species
 included within this study. Supplementary Data
 2 Completeness scores used to calculate SCM.
 Supplementary Data 3 Completeness scores
 used to calculate BSCM. Supplementary Data
 4 References used to estimate body size for each
 species. Supplementary Data 5 Mean
 averages, medians and standard deviations for spatiotemporal completeness
 values. Supplementary Data 6
 Statistical test results. Supplementary Data
 7 Phylogenetic and stratigraphic congruence
 results. Supplementary Data 8
 Phylogenetic and stratigraphic congruence results.
DOI: 10.5061/dryad.crjdfn32m
title: A revised subgeneric classification of the neotropical genus Zapoteca (Caesalpinioideae; Fabaceae)

description: The subgeneric classification of the neotropical legume
 genus Zapoteca is revised based on an analysis of the
 nuclear ETS and ITS, and the
 plastid trnL-trnF DNA-regions.
 Subgenus Ravenia is included in
 subg. Zapoteca, Z. quichoi is
 transferred from subg. Amazonica to
 subg. Zapoteca, Z. sousae is included
 in subg. Zapoteca and one new subgenus,
 subg. Subamazonica, is described to accommodate the
 species Z. filipes and Z. scutellifera. A key to the subgenera is presented.
description: Multiple DNA-sequence alignments of ETS, ITS and trnL-trnF of the
 neotropical genus <em>Zapoteca</em> (Fabaceae) and tree files
 resulting from Bayesian inference analyses.
DOI: 10.25338/b8n03h
title: A preliminary framework for magmatism in modern continental back-arc basins and its application to the Triassic-Jurassic tectonic evolution of the Caucasus

description: In contrast to intraoceanic back-arc basins, extension within a
 continental back-arc basin initiates within continental rather than
 oceanic lithosphere. The geochemical characteristics of magmatic rocks
 within continental back-arc basins are poorly understood relative to their
 intraoceanic counterparts. Here, we compile published geochemical data
 from five modern continental back-arc basins – the Okinawa Trough,
 Bransfield Strait, Tyrrhenian Sea, Patagonia plateau, and Aegean
 Sea/Western Anatolia – to establish a geochemical framework for
 continental back-arc magmatism.  This analysis shows that
 continental back-arcs yield geochemical signatures more similar to arc
 magmatism than intraoceanic back-arcs. We apply this framework to
 published data for Triassic-Jurassic magmatic rocks from the Caucasus arc
 system, which includes a relict continental back-arc basin, the Caucasus
 Basin, that opened during the Jurassic and for which the causal mechanism
 of formation remains unexplained. 40Ar/39Ar and U-Pb ages indicate
 Permian-Triassic arc magmatism from ~260-220 Ma due to subduction beneath
 the Greater Caucasus and Scythian Platform. Late Triassic (~220-210 Ma)
 collision of the Iranian block with Laurasia likely induced trench retreat
 in the Caucasus region and led to migration of the Caucasus arc front and
 opening of the Caucasus Basin. This activity was followed by Jurassic
 magmatism in the Caucasus Basin from ~180-160 Ma and in the Lesser
 Caucasus arc from ~180-140 Ma. Trace element and Sr-Nd isotopic data for
 magmatic rocks indicate that Caucasus Basin magmatism is comparable to
 modern continental back-arcs and that the mantle source to the Lesser
 Caucasus arc became more enriched at ~160 Ma, likely from the cessation of
 back-arc spreading.
description: This dataset contains the Supporting Information for the
 manuscript entitled "A preliminary framework for magmatism in modern
 continental back-arc basins and its application to the Triassic-Jurassic
 evolution of the Caucasus."  A description of the
 contents of the dataset can be found in the main Word document:<br>
     Vasey_CaucArc_SupportingInformation.docx