cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bg79cnp83
title: Data from: Cooperation can promote rescue or lead to evolutionary suicide during environmental change

description: The adaptation of populations to changing conditions may be affected by
 interactions between individuals. For example, when cooperative
 interactions increase fecundity, they may allow populations to maintain
 high densities and thus keep track of moving environmental optima.
 Simultaneously, changes in population density alter the marginal
 benefits of cooperative investments, creating a feedback loop between
 population dynamics and the evolution of cooperation. Here we
 model how the evolution of cooperation interacts with adaptation
 to changing environments. We hypothesize that environmental change lowers
 population size and thus promotes the evolution of cooperation,
 and that this, in turn, helps the population keep up with
 the moving optimum. However, we find that the evolution of
 cooperation can have qualitatively different effects, depending
 on which fitness component is reduced by the costs of cooperation. If the
 costs decrease fecundity, cooperation indeed speeds adaptation by
 increasing population density; if, in contrast, the costs
 decrease viability, cooperation may instead slow adaptation by
 lowering the effective population size, leading to evolutionary
 suicide. Thus, cooperation can either promote
 or—counter-intuitively—hinder adaptation to a changing
 environment. Finally, we show that our model can also be generalized to
 other social interactions by discussing the evolution of
 competition during environmental change.
description:  
description: This repository includes: 
 A <em>Mathematica</em> notebook with all the
 calculations required to replicate the results presented in the paper and
 in its Supplemental Information. For users
 without <em>Mathematica</em>, we also include the
 corresponding .cdf notebook and .pdf file. A set
 of <em>R </em>scripts with the code the individual-based
 simulations, as well as the data generated by these scripts and used in
 the paper.
DOI: 10.5068/d16t06
title: Data from: From lidar waveforms to vegetation products: 7380 km2 of high-resolution airborne and simulated GEDI data over Sierra Nevada, California

description: Vegetated ecosystems have complex three-dimensional (3D) canopy structures
 with diverse plant type assemblages, crown architectures and historical
 disturbances. Vegetation structure changes dramatically with strong
 topographic, edaphic and climate gradients. Airborne lidar remote sensing
 has the potential to measure fine-scale 3D proprieties of forests with
 limited temporal and spatial coverage limitations due to prohibitively
 cost. Here, we present a composite high-resolution airborne lidar dataset
 covering 7380 km2 over the Sierra Nevada, California, that has been
 calculated from a time-series (2014-2017) collected by the NASA-JPL
 Airborne Snow Observatory (ASO). We coherently merge low resolution (~1 pt
 m-2) ASO lidar measurements, primarily acquired to quantify snow volume
 and dynamics, to produce high-resolution point clouds that better describe
 forest structure and underlying topography (Ferraz et al., 2016). The
 methodology addresses the removal of lidar points corresponding to snow
 cover as well as the spatial bias in multi-temporal data due to
 uncertainties in platform trajectory and motion. We then derived many
 user-friendly raster products on 3D forest structure (relative heights,
 plant area index, foliage height diversity), forest functional diversity
 (richness, evenness, beta diversity) and topographic indexes (topographic
 wetness index, terrain ruggedness, slope) with spatial resolutions varying
 from 10 m to 1 km. Our dataset enables the study of landscape-scale
 studies on a myriad of applications (carbon storage, habitat niche and
 quality, hydrology, fire hazard and behavior,) over a large region rich in
 forest types diversity (e.g. alpine, montane, sub-montane forests), with
 contrasting land uses (e.g. protected vs managed forest) and well
 documented historical disturbances (e.g. fire). 
description:       The methods to describe the composite ASO lidar point
 clouds are descirbed in        Ferraz, A., Saatchi, S.,
 Bormann, K.J., Painter, T.H. (2018). Fusion of NASA Airborne Snow
 Observatory (ASO) Lidar Time Series over Mountain Forest Landscapes.
 Remote Sensing, 10, 164.       To methods to produce
 the raster products on forest 3D structure, underlying topography
 and forest functional diversity are described in :
       Schneider, F., Ferraz, A., Hancock, S., Duncanson, L.,
 Dubayah, R., Pavlick, R., Schimel, D. (in review). Towards mapping the
 diversity of canopy structure from space with GEDI. Environmental Research
 Letters    
description: Metadata files have been included in the repository
DOI: 10.5061/dryad.wdbrv15kn
title: Data from: Conservation concern among Australian undergraduates is associated with childhood socio-cultural experiences

description: Fostering widespread concern for conservation problems requires a robust
 understanding of the life experiences that positively contribute to an
 individual's conservation attitudes and behaviours. However, few
 studies have assessed a comprehensive range of social and experiential
 predictors of conservation concern. Using survey responses from 391
 undergraduate students enrolled in various course disciplines across
 Australia, we describe the relationship between five major constructs of
 early-life experiences and two measures of conservation concern: a
 preference for conservation career, and positive conservation attitudes.
 We find that conservation career preferences are positively associated
 with childhood preferences for nature-related books, movies and school
 subjects, biospheric family value orientations and environmental
 volunteering. Conseravtion attitudes were postitively associated with
 biospheric family value orientations and environmental volunteering. Both
 constructs were negatively associated with egoistic family values, and
 childhood experiences in nature were not a significant factor in either of
 our models. This suggests that limited nature experiences do not
 necessarily impede the development of conservation concern in young
 Australians, which was strongly related to the values of their immediate
 family and their experiences with environmental organisations,
 nature-related storylines and school subjects.
description: This dataset was collected in accordance with the National
 Statement of Ethical conduct in Human Research ethics under the guidelines
 and processes of the University of Queensland Human Research Ethics
 Approval (2018/001857). Researchers approached participants through social
 media by accessing university groups over Facebook. Between 27 September
 and 14 October 2018, 500 Austrlaian undergraduate students responded to
 our questionnaire via SurveyMonkey.
description: While the focus of our research was nature-related experiences
 and conservation behaviour, this dataset collated information on a wide
 variety early-life experiences (across 5 domains of nature exposure,
 education, organisations, cultural narratives and family values) and
 surveyed students from a broad range of course disciplines including
 health and law.
DOI: 10.5061/dryad.tdz08kpwz
title: Novel immunoassay detecting p-Tau Thr217 distinguishes Alzheimer’s Disease from other dementias

description: Objective To investigate whether p-tau T217 assay in cerebrospinal fluid
 (CSF) can distinguishes Alzheimer’s disease from other dementias and
 healthy controls. Methods We developed and validated a novel Simoa
 immunoassay to detect p-tau T217 in CSF. There was a total of 190
 participants from three cohorts with AD (n = 77) and other
 neurodegenerative diseases (n = 69) as well as healthy subjects (n = 44).
 Results The p-tau T217 assay (cut-off 242 pg/ml) identified AD subjects
 with accuracy of 90%, with 78% positive predictive value (PPV), 97%
 negative predictive value (NPV), 93% sensitivity, 88% specificity compared
 favorably with p-tau T181 ELISA  (52 pg/ml) showing 78% accuracy,
 58% PPV, 98% NPV, 71% specificity; 97% sensitivity. The assay
 distinguished AD patients from age-matched healthy subjects (cut-off 163
 pg/ml, sensitivity 98%, specificity 93%) similarly to p-tau T181 ELISA
 (cut-off 60 pg/ml, 96% sensitivity and 86% specificity). In AD patients,
 we found a strong correlation between p-tau T217-tau and p-tau T181, t-tau
 and Aβ40 but not with Aβ42. Conclusions This study demonstrates that p-tau
 T217 displayed better diagnostic accuracy than p-tau T181. The data
 suggests that new p-tau T217 assay has a potential as an AD diagnostic
 test in the clinical evaluation. Classification of Evidence: 
 This study provides Class III evidence that a CSF immunoassay for p-tau
 T217 distinguishes AD from other dementias and healthy controls.
DOI: 10.5061/dryad.1ns1rn8r3
title: Apolipoprotein L-1 renal risk variants form active channels at the plasma membrane driving cytotoxicity

description: Recently evolved alleles of Apolipoprotein L-1 (APOL1) provide increased
 protection against African trypanosome parasites while also significantly
 increasing the risk of developing kidney disease in humans. APOL1 protects
 against trypanosome infections by forming ion channels within the
 parasite, causing lysis. While the correlation to kidney disease is
 robust, there is little consensus concerning the underlying disease
 mechanism. We show in human cells that the APOL1 renal risk variants have
 a population of active channels at the plasma membrane, which results in
 an influx of both Na+ and Ca2+. We propose a model wherein APOL1 channel
 activity is the upstream event causing cell death, and that the
 activate-state, plasma membrane-localized channel represents the ideal
 drug target to combat APOL1-mediated kidney disease.
DOI: 10.5061/dryad.2280gb5p9
title: Independent evolutionary changes in fine-root traits among main clades during the diversification of seed plants

description: Rationale: Changes in fine-root morphology are typically associated with
 transitions from the ancestral arbuscular mycorrhizal (AM) to the
 alternative ectomycorrhizal (ECM) or non-mycorrhizal (NM) associations.
 However, the modifications in root morphology may also coincide with new
 modifications in leaf hydraulics and growth habit during angiosperm
 diversification. These hypotheses have not been evaluated concurrently,
 which limits our understanding of the causes of fine-root evolution.
 Methods: To explore the evolution of fine-root systems, we assembled a
 600+ species database to reconstruct historical changes in seed plants
 over time. We utilize ancestral reconstruction approaches together with
 phylogenetically informed comparative analyses to test whether changes in
 fine-root traits were most strongly associated with mycorrhizal
 affiliation, leaf hydraulics or growth form. Key Results: Our findings
 show significant shifts in root diameter, specific root length and root
 tissue density as angiosperms diversified, largely independent from leaf
 changes or mycorrhizal affiliation. Growth form was the only factor
 associated with fine-root traits in statistical models including
 mycorrhizal association and leaf venation, suggesting substantial
 modifications in fine-root morphology during transitions from woody to
 non-woody habits. Conclusion: Divergences in fine-root systems were
 crucial in the evolution of seed plant lineages, with important
 implications for ecological processes in terrestrial ecosystems.
description: In the case of leaf vein density, we compiled information from
 Boyce <i>et al.</i> 2009 (257 species); Brodribb &
 Feild 2010 (272 species); Walls 2011 (87 species) and Li <i>et
 al.</i> 2015 (80 species, see Notes 1 for a detailed list). Because
 “vein density” is defined as the average distance between veins (usually
 secondary and higher orders) within the mesophyll (Brodribb, Feild
 & Sack 2010), taxa with single-veined leaves like gymnosperms or
 parallel venation like most monocots were under-represented in this
 dataset. In the case of root traits, we used data described in
 Valverde-Barrantes <i>et al.</i> (2017) for diameter (D, mm),
 SRL (g/m), and RTD (g/cm<sup>3</sup>) deposited in the Fine
 Root Ecological Database (FRED; Iversen <i>et al.</i> 2017,
 2018). Habit classification was obtained directly from the FRED database
 dividing the species between woody shrubs, trees and non-woody herbs.
 Mycorrhizal state was binned into four mycorrhizal groups based on the
 classification in Maherali <i>et al.</i> (2016): AM, ECM,
 transitional (AMNM) and non-mycorrhizal (NM) based on consensus
 classification from previous studies. Species reported as AM or NM in
 different studies were binned in the AMNM transitional stage (Maherali
 <i>et al.</i> 2016).
DOI: 10.5061/dryad.x3ffbg7g4
title: Comparing diversification rates in lakes, rivers, and the sea

description: The diversity of species inhabiting freshwater relative to marine habitats
 is striking, given that freshwater habitats encompass &lt;1% of
 Earth’s water. The most commonly proposed explanation for this pattern is
 that freshwater habitats are more fragmented than marine habitats,
 allowing more opportunities for allopatric speciation and thus increased
 diversification rates in freshwater. However, speciation may be generally
 faster in sympatry than in allopatry, as illustrated by lacustrine
 radiations such as African cichlids. Differences between rivers and lakes
 may be important to consider when comparing diversification broadly among
 freshwater and marine lineages. Here I compared diversification rates of
 teleost fishes in marine, riverine and lacustrine habitats. I found that
 lakes had faster speciation and net diversification rates than other
 aquatic habitats. However, most freshwater diversity arose in rivers.
 Surprisingly, riverine and marine habitats had similar rates of net
 diversification. Biogeographic models suggest that lacustrine habitats are
 evolutionary unstable, explaining the dearth of lacustrine species in
 spite of their rapid diversification. Collectively, these results suggest
 that diversification rate differences are unlikely to explain the
 freshwater paradox. Instead, this pattern may be attributable to the
 comparable amount of time spent in riverine and marine habitats over the
 200-million-year history of teleosts.
DOI: 10.5061/dryad.pzgmsbchf
title: Data from: Multi-population seedling and soil transplants show possible responses of a common tropical montane tree species (Weinmannia bangii) to climate change

description: A possible response of many plant species to global warming is migration
 to higher elevations. However, these migrations may not be required if
 species can tolerate higher temperatures, or may be prevented if there are
 other factors such as changes in soil conditions that make upslope areas
 unsuitable. We used a set of 3-year field transplant experiments in the
 remote Peruvian Andes to simulate two possible responses of an abundant
 tropical montane cloudforest tree species (Weinmania bangii) to global
 warming: (1) “upward migration”, in which case seedlings of W. bangii’s
 were grown at their current elevation/temperature but in soils
 transplanted from higher elevations; and (2) “migration failure”, in which
 case seedlings were transplanted downslope along with their home soils
 into areas that are 1°C or 2°C warmer. We conducted separate experiments
 with populations from the upper/leading edge, middle and lower/trailing
 edges of W. bangii’s elevational/thermal range to assess the influence of
 local adaptation on responses to changes in temperature or soil. We found
 that seedling survival and growth were not affected by changes in soil
 conditions, regardless of the origin population. However, seedling
 survival decreased with temperature. A simulated warming of 1°C caused a
 significant reduction in the survival of seedlings transplanted from the
 mid-range population, and 2°C warming caused a severe decrease in the
 survival of seedlings transplanted from both the mid-range and bottom-edge
 populations. Synthesis. Our findings reveal that rising temperatures are a
 serious threat to plants, especially in populations growing in the hotter
 portion of their species’ range. At least in the case of W. bangii, novel
 soil conditions will not limit the establishment or growth of seedlings at
 higher elevations. As such, decreases in the survivorship at lower
 elevations may be offset through upward migrations as temperatures
 continue to increase.
description: <strong>growth_herbivory_stress</strong>
 This file contains data on seedling growth rate, herbivory, and
 index of physiological stress.
 <strong>survival_migration_failure</strong> and
 <strong>survival_upward_migration</strong>
 These files contain data on seedling survival for "migration
 failure" and "upward migration" treatments,
 respectively.
DOI: 10.5061/dryad.kprr4xh28
title: Controls on range shifts of coastal Californian bivalves during the peak of the last interglacial and baseline predictions for today

description: As the most recent time in Earth history when global temperatures were
 warmer than at present, the peak of the last interglacial (Marine Isotope
 Substage [MIS] 5e; ~120,000 years ago) can serve as a pre-anthropogenic
 baseline for a warmer near-future world. Here we use a new compilation of
 22 fossil localities in California that have been reliably dated to Marine
 Isotope Stage (MIS) 5e to establish baseline expectations for contemporary
 bivalve species movements by identifying and analyzing bivalve species
 with “extralimital” ranges, i.e. species that occupied the California
 region during MIS 5e but are now restricted to adjacent regions. We find
 that 15% of species (n = 142) found in MIS 5e localities have extralimital
 ranges and currently occupy warmer waters to the south of the California
 region. The majority of extralimital occurrences occur in
 paleo-embayments, suggesting that these sheltered habitats were more
 suitable habitats for warm-water species than exposed coasts during the
 MIS 5e. We further find that extralimital species now tend to occur in
 cooler, more seasonally productive coastal waters and to occupy more
 offshore islands when compared to the broader species pool immediately
 south of California. These findings suggest that high dispersal potential
 and pre-existing tolerances to environmental conditions similar to
 California’s comparatively cool and seasonally productive environments may
 have enabled extralimital bivalves to colonize the California region
 during MIS 5e.
description: <strong>Appendices_1-3.xlsx </strong>
 Data appendices formatted for readability and reference. Sheets
 1-6 contain data, data sources, and descriptions for each file included as
 headings. All methods to generate appendices are described in Orzechowski
 and Finnegan 2020.<strong> </strong>
 <strong>SI_analyses.R</strong> R
 code to reproduce manuscript analyses, tables, and figures.<strong>
 </strong>Data necessary for reproduction are:
 "SI_coasts.csv", "SI_fauna_range_limits.csv", and
 "SI_fauna_range_through.csv". These files are described in
 "SI_files_description.txt."
 <strong>SI_coasts.csv</strong>
 Fossil localities classified as (paleo) embayment or open coast;
 presence or absence of extralimitals at each locality indicated.
 <strong>SI_fauna_range_limits.csv</strong>
 Range-limiting environmental variables for species
 analyzed.
 <strong>SI_fauna_range_through.csv</strong>
 Range-through environmental variables for species
 analyzed.
 <strong>SI_files_description.txt</strong>
 Description of "SI" files, with key for each
 column.
DOI: 10.5061/dryad.dncjsxkwn
title: Longitudinal changes in the retinal microstructures of eyes with chiasmal compression

description: Objective: To test the hypothesis that there was a temporal change in the
 retinal microstructure after decompression surgery for chiasmal
 compression, the 1-year longitudinal changes in the inner and outer
 retinal thickness after decompression surgery were analyzed using
 spectral-domain optical coherence tomography (SD-OCT) with linear
 mixed-effects models. Methods: SD-OCT was obtained from 87 eyes with
 chiasmal compression and compared to 100 healthy controls. The
 preoperative and 1-year postoperative longitudinal changes in the retinal
 layer thickness were measured. The thickness of each of the following
 retinal layers was analyzed: the macular retinal nerve fiber layer (RNFL),
 the ganglion cell layer (GCL), the inner plexiform layer (IPL), the inner
 nuclear layer, the outer plexiform layer, the outer nuclear layer, and the
 photoreceptor layer. Results: The RNFL, GCL, and IPL showed thinning at a
 rate of 1.068 μm/year (95% confidence interval [CI], 0.523, 1.613), 1.189
 μm/year (95% CI, 0.452, 1.925), and 1.177 μm/year (95% CI, 0.645, 1.709),
 respectively, after decompression surgery. The preoperative thickness of
 the intra-retinal layer was associated with postoperative visual field
 (VF) recovery (RNFL, odds ratio [OR] = 1.221, 95% CI, 1.058, 1.410; GCL,
 OR = 1.133, 95% CI, 1.024, 1.254; and IPL, OR = 1.174, 95% CI, 1.002,
 1.376). Conclusions: The changes in retinal microstructure persisted and
 progressed in eyes with chiasmal compression after decompression surgery.
 The findings provide insight into the biological and anatomical sequelae
 following chiasmal compression. The preoperative thickness of the inner
 retinal layers was associated with postoperative VF recovery.
DOI: 10.5061/dryad.vx0k6djnz
title: A fossil-calibrated time-tree of all Australian freshwater fishes

description: Australian freshwater fishes are a relatively species-poor assemblage,
 comprising a small number of Gondwanan lineages and a number of groups
 derived from repeated freshwater invasions by marine ancestors. In
 addition to being a comparatively small assemblage, they are both highly
 endemic and highly threatened. However, a comprehensive phylogeny for
 these taxa is lacking, which has hampered efforts to study their
 phylogenetic diversity, distribution of extinction risk, speciation rate,
 and rates of trait evolution. Here, we present a comprehensive dated
 phylogeny of 412 Australian freshwater fishes. We include all formally
 recognized freshwater species plus a number of genetically distinct
 subpopulations, species awaiting formal description, and predominantly
 brackish-water species. The phylogeny was inferred using
 maximum-likelihood analysis of a multilocus data set comprising six
 mitochondrial and three nuclear genes from 326 taxa. We inferred the
 evolutionary timescale using penalized likelihood, then used a statistical
 approach to add 86 taxa for which no molecular data were
 available. The time-tree inferred in our study will provide a
 useful resource for macroecological studies of Australian freshwater
 fishes, by enabling corrections for phylogenetic non-independence in
 evolutionary and ecological comparative analyses.