cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7291/d1rq46
title: Data from: Factors explaining variability in woody above-ground biomass accumulation in restored tropical forest

description: Secondary forests comprise an increasing area of the tropics and play an
 important role in global carbon cycling. We compare above-ground biomass
 accumulation of both planted and naturally regenerating trees, as well as
 C in the top soil layer, in three restoration treatments replicated at 14,
 six to eight year old restoration sites in southern Costa Rica.
 Restoration strategies include: control (no planting), planting tree
 islands, and conventional, mixed-species tree plantations. We evaluate the
 importance of past land-use, soil nutrients, understory cover, and
 surrounding forest cover in explaining variation in above-ground biomass
 accumulation (ABA) rate across sites. Total ABA and planted tree ABA rate
 were highest in plantations, intermediate in islands, and lowest in
 control treatments, whereas ABA rate of naturally regenerating trees did
 not differ across treatments. Most ABA in plantations (89%) and islands
 (70%) was due to growth of planted trees. Soil carbon did not change
 significantly over the time period of the study in any treatment. The
 majority of across-site variation in both total and planted tree ABA rate
 was explained by duration of prior pasture use. Tree growth in the first
 two years after planting explained approximately two-thirds of the
 variation in ABA rate after 6–8 years. Soil nutrient
 concentrations explained relatively little of the variation in planted or
 naturally recruiting ABA rate. Our results show that planting trees
 substantially increases biomass accumulation during the first several
 years of forest recovery in former agricultural lands and that past-land
 use has a strong effect on the rate of biomass accumulation. Planting tree
 islands is a cost-effective strategy for increasing ABA and creating more
 heterogeneous habitat conditions than tree plantations. We recommend small
 scale planting trials to quickly assess potential biomass accumulation and
 prioritize sites for ecosystem service payments for carbon sequestration.
description: Data were collected in May-July of each year.  Trees were
 recorded as dead (0), alive (1), or cut (c); cut seedlings were
 accidentally cut during clearing of ruderal vegetation or trails.  Tree
 height was measured to the nearest centimeter using a measuring tape
 or measuring poles (2004-2007) and a laser range finder (2008-2012).  DBH
 was measured to the nearest mm using a DBH tape.  Tree DBH and cover were
 measured on all living trees in island treatments and on randomly selected
 trees in the plantation treatment. Canopy cover was measured by measuring
 the distance of two perpendicular lines to the nearest 5 cm and using the
 formula for an ellipse (see Holl et al. 2011).  <br>
DOI: 10.7291/d1mx1w
title: Site description

description: Descriptions of 15 original sites from Islas project. Used in various
 publications and described in Holl, K. D., J. L. Reid, R. J. Cole, F.
 Oviedo-Brenes, J. A. Rosales, and R. A. Zahawi. 2020. Applied nucleation
 facilitates tropical forest recovery: Lessons learned from a 15-year
 study. Journal of Applied Ecology 57:2316-2328.
description: Slope was measured using a hand held clinometer and aspect was
 measured using Suunto sighting compass.  The location of each of the
 corners of the plots were measured using a Trimble GPS with &lt;1 m
 accuracy and the centroid of each polygon calculated.  Elevations are
 averages of the elevations of the corner plots.
description: See "Site description.txt" for more details.
DOI: 10.7291/d1h670
title: Data from: Scale-dependent effects of forest restoration on Neotropical fruit bats

description: Neotropical fruit bats (family Phyllostomidae) facilitate forest
 regeneration on degraded lands by dispersing shrub and tree seeds.
 Accordingly, if fruit bats can be attracted to restoration sites, seed
 dispersal could be enhanced. We surveyed bat communities at 10 sites in
 southern Costa Rica to evaluate whether restoration treatments attracted
 more fruit bats if trees were planted on degraded farmlands in plantations
 or island configurations versus natural regeneration. We also compared the
 relative influence of tree cover at local and landscape spatial scales on
 bat abundances. We captured 68% more fruit bat individuals in tree
 plantations as in controls, whereas tree island plots were intermediate.
 Bat activity also responded to landscape tree cover within a 200‐m radius
 of restoration plots, with greater abundance but lower species richness in
 deforested landscapes. Fruit bat captures in controls and tree island
 plots declined with increasing landscape tree cover, but captures in
 plantations were relatively constant. Individual species responded
 differentially to tree cover measured at different spatial scales. We
 attribute restoration effects primarily to habitat structure rather than
 food resources because no planted trees produced fruits regularly eaten by
 bats. The magnitude of tree planting effects on fruit bats was less than
 previous studies have found for frugivorous birds, suggesting that bats
 may play a particularly important role in dispersing seeds in heavily
 deforested and naturally regenerating areas. Nonetheless, our results show
 that larger tree plantations in more intact landscapes are more likely to
 attract diverse fruit bats, potentially enhancing seed dispersal.
description: In 2009, Chase Mendenhall (Stanford) led the sampling effort. 13
 of the Islas restoration plots were sampled with three 12-m ground-level
 mist-nets per plot (3 plots per site). Mist-nets were placed along
 previously determined lanes. Each site was sampled for one night; nets
 were opened at dusk (~6PM) and kept open for four hours. In 2012, Leighton
 Reid (University of California Santa Cruz) led the sampling effort. Ten
 Islas sites were sampled with three 6-m ground-level mist-nets per plot (3
 plots per site). Five mature reference forests sites were also sampled
 with three ground-level mist-nets per reference forest. Mist-nets were
 placed advantageously within flyways, but were evenly distributed
 throughout plots. Each net was paired with a permanent vegetation sampling
 transect. Mist-nets in areas with dense ground vegetation (i.e., grass or
 bracken fern) were elevated to just above the level of the vegetation
 using extendable painter poles. Mist nets were opened at dusk (~6PM) and
 kept open for four hours. Each site was sampled twice.
DOI: 10.5061/dryad.qz612jmff
title: Landform type mediates compositional change in a hurricane-disturbed sub-tropical forest

description: This data describes the species composition of trees over time in plots
 located within the Jardín Botánico and Bosque Estatal del Nuevo Milenio on
 the island of Puerto Rico.  The field sites were established in
 1997 by Despiau Batista and the data collected in 1997 was used in Despiau
 Batista, 1997.  These field sites were revisited in 2005 with the
 new tree data being used by Lugo et al., 2005.  The species data
 from 1997 was compared to that of 2005 in Spicer et al., 2020 and the data
 included here are those used by Spicer et al.  The works of
 Despiau Batista (1997) and Lugo et al (2005) do not have associated
 DOI's.    Despiau Batista A (1997) Distribución de
 las especies arbóreas de acuerdo al gradiente en topografía en el bosque
 de Río Piedras, Puerto Rico, luego de 60 años de abandono agrícola. Acta
 Científica 11:3–20 Lugo AE, Román Nunci E, Quiñones M, Marcano Vega H,
 Vicéns I (2005) El bosque estatal del nuevo milenio antes y después del
 huracán Georges. Acta Cientifica 19(1-3):83–105 Spicer RL, Lugo AE, and
 Ruhl N.  (2020) Landform types mediates compositional change in a
 hurricane disturbed sub-tropical forest.  Ecological Processes,
 9, 26.  
description: The 1997 data was collected during June/July.  10 plots were
 randomly located within each of four different landform types (40 plots
 total).  All of these plots were located on a similar aspect facing
 southwest and ranged in elevation from 15-65m.  Plot size was consistent
 across the study (254 square meters) with two sites being rectangular and
 the rest being circular.  Trees were tagged, identified, and measured for
 height using a clinometer if they had a diameter at brest-height of
 greater than 4cm.  These sites were revisited in August/September 2005 and
 the species composition and height of trees within each plot were
 remeasured.
description: Landform type was not recorded for a few sites.  Tree heights are
 sometimes not recorded.
DOI: 10.7291/d1cd6f
title: Soil nutrients

description: Surface soil nutrients collected in 2007, 2012, 2017 from research plots
 described in Holl, K. D., J. L. Reid, R. J. Cole, F. Oviedo-Brenes, J. A.
 Rosales, and R. A. Zahawi. 2020. Applied nucleation facilitates tropical
 forest recovery: Lessons learned from a 15-year study. Journal of Applied
 Ecology 57:2316-2328 (https://doi.org/10.1111/1365-2664.13684).
description: In July-Aug 2007 and June-July 2012 and 2017 we collected
 twenty-five 2.5-cm diameter × 15-cm deep soil cores across each 50 x 50 m
 plot. Cores were mixed, passed through a 2-mm sieve and air dried prior to
 analysis. In 2007, 2012, and 2017 samples were analyzed for organic
 matter, Bray and Mehlich III P, and cations and micronutrients using
 Mehlich III extractions following standard procedures at Brookside
 Laboratories, Knoxville, Ohio (see
 https://www.blinc.com/resources/testing-methods for details on protocols).
 In 2007 a small sample was finely ground, and C and N were determined by
 Dumas combustion using a Carlo Erba 1108 elemental analyzer at the
 University of California, Santa Cruz Stable Isotope Laboratory – see
 http://es.ucsc.edu/~silab/index.php. In 2012 and 2017 C:N ratios were
 analyzed at Brookside Laboratories.
description: Name of data files in data set: 
 Soil – nutrients – 2007 – Brookside Labs
 Soil – nutrients – 2012 – Brookside Labs
 Soil – nutrients – 2012 – Brookside Labs
 Soil – CNisotopes – 2007 – UCSC Lab Soil –
 CN – 2012 – Brookside Labs Soil – CN – 2012 –
 Brookside Labs See read.me file for more
 details.
DOI: 10.25338/b8sh0s
title: Scaling up experimental stress responses of grass invasion to predictions of continental-level range suitability

description: Understanding how the biological invasion is driven by environmental
 factors will improve model prediction and advance early detection,
 especially in the context of accelerating anthropogenic ecological
 changes. Although a large body of studies has examined how favorable
 environments promote biological invasions, a more comprehensive and
 mechanistic understanding of invasive species response to
 unfavorable/stressful conditions is still developing. Grass invasion has
 been problematic across the globe; in particular, C4 grass
 invaders, with high drought tolerance, adaptations to high temperatures,
 and high water use efficiency, could become more severe. Here, we
 conducted a rigorous microcosm experiment, with one of the most damaging
 invasive C4 grass - cogongrass (Imperata cylindrica), to explore
 how cogongrass responds to soil water and nutrient stress. We further
 integrated the results of the microcosm study with a species distribution
 model to (1) corroborate greenhouse results with field observations and
 (2) validate the robustness of our findings at sub-continental scales.
 Both the microcosm experiments and species distribution model agreed that
 soil water stress had a stronger impact on cogongrass than the nutrient
 one. New vegetative growth of cogongrass continued to be inhibited by the
 prior water stress. The significant water effect on cogongrass total
 biomass was supported by the finding that both allometric and biochemical
 traits of cogongrass did not show significant responses to the changes in
 water treatment. Different to the conventional wisdom that nutrient
 enrichment plays a bigger role in facilitating biological invasions, this
 study highlighted the possibility that water conditions may have a more
 substantial effect on some aggressive invaders. Therefore, an important
 implication of this study on biological conservation is that field
 managers might take advantage of the negative effect of global drought on
 some invasive species to increase the efficiency of their controlling
 efforts because invasive species may become more vulnerable under drought
 effect.
description: The data were collected in a greenhouse experiment.
DOI: 10.5061/dryad.r7sqv9sc1
title: The transcriptome unigenes of Vicia faba

description: 243,120 unigenes were de novo assembled from flowers and leaves of 102
 domestic and foreign broad bean accessions.
DOI: 10.5061/dryad.gmsbcc2n8
title: Data from: A phantom ultrasonic insect chorus repels low-flying bats, but most are undeterred

description: Abstract 1. The acoustic environment can serve as a niche axis,
 structuring animal behaviour by providing or obscuring salient
 information. Meadow katydid choruses occupy the ultrasonic, less studied,
 realm of this acoustic milieu, form dense populations in some habitats,
 and present a potential sensory challenge to co-occurring
 ultrasonic-hearing animals. Aerial-hawking insectivorous bats foraging
 immediately over vegetation must listen for echoes of their prey and other
 cues amidst the chorus din. 2. We experimentally created the cacophony of
 a katydid chorus in a katydid-free rice paddy using an aggregation of 100
 ultrasonic speakers in a 25 x 25 m grid to test the hypothesis that
 aerially hawking bats are averse to this noise source. We alternated
 between chorus-on and chorus-off hourly, and acoustically monitored bat
 activity and arthropod prey abundance. 3. We found that our phantom
 katydid chorus reduced bat activity nearest the sound source by 39.3% (95%
 CI: 7.8 - 60.0%) for species whose call spectrum fully overlapped with the
 chorus, and elicited marginal reductions in activity in species with only
 partial spectral overlap. 4. Our study suggests that ultrasonic insect
 choruses degrade foraging habitat, potentially suppressing bats’ ecosystem
 services as consumers of pests; and, given the global distribution of
 meadow katydids, may provide an underappreciated force modifying animal
 behaviour in other grassland habitats.
DOI: 10.5061/dryad.6wwpzgmzf
title: Development and application of Faba_bean_130K Targeted Next-Generation Sequencing SNP genotyping platform based on transcriptome sequencing

description: Faba bean (Vicia faba L., 2n = 12) is an important food legume crop and
 widely grown for multiple uses in the world. However, no reference genome
 is currently available due to its giant genome (approximately 13 Gb) and
 limited single nucleotide polymorphism (SNP) markers as well as high
 efficient genotyping tools have been reported for faba bean. In this
 study, 16.7 billion clean reads were obtained from transcriptome libraries
 of flowers and leaves of 102 global faba bean accessions. 243,120 unigenes
 were de novo assembled and functionally annotated. Moreover, a total of
 1,579,411 SNPs were identified and were further filtered according to a
 selection pipeline to develop a high-throughput, flexible and low-cost
 Faba_bean_130K Targeted Next-Generation Sequencing (TNGS) genotyping
 platform. A set of 69 Chinese faba bean accessions was genotyped with the
 TNGS genotyping platform, and the average mapped rate of captured reads to
 reference transcripts was 93.14%, of which 53.23% were located in the
 targeted regions. The TNGS genotyping results were validated by Sanger
 sequencing and the average consistency rate was up to 93.6%. Comprehensive
 population genetic analyze was performed to the 69 Chinese faba bean
 germplasm and identified four genetic subgroups correlated with geographic
 distribution. This study provides valuable genomic resources and a
 reliable genotyping tool, which could be implemented in genetic and
 molecular breeding studies to accelerate the faba bean new cultivar
 development and improvement.
DOI: 10.5061/dryad.59zw3r273
title: Supplementary materials for: Influence of cognitive reserve on cognitive trajectories: role of brain pathologies

description: Background and Objectives: Evidence on the association of the cognitive
 reserve (CR) with the cognitive trajectories is limited. We aimed to
 examine the influence of CR indicator on domain-specific cognitive
 trajectories taking brain pathologies into account. Methods: Within the
 Rush Memory and Aging Project, 1,697 dementia-free participants (mean age:
 79.6 years) were followed up to 21 years. CR indicator encompassing
 education, early-life, mid-life, and late-life cognitive activities, and
 late-life social activity was ascertained at baseline and categorized as
 tertiles (the lowest, middle, and highest). Global cognition, episodic
 memory, semantic memory, working memory, visuospatial ability, and
 perceptual speed were assessed annually with 19 tests, from which
 composite scores were derived. During the follow-up, 648 died and
 underwent autopsies to evaluate brain pathologies. Data were analyzed
 using linear mixed-effect models. Results: Among the participants, the
 score of the CR indicator ranged from -8.00 to 5.74 (mean: 0.00±2.23). In
 multi-adjusted mixed-effect models, compared to the lowest CR, the highest
 was related to a slower decline in global cognition (β=0.028, 95%
 confidence interval [CI]: 0.012 to 0.043), episodic memory (β=0.028, 95%
 CI: 0.010 to 0.047) and working memory (β=0.019, 95% CI: 0.005 to 0.033)
 during the follow-up. In brain pathological data analysis, the association
 of the highest CR with cognitive function changes remained significant
 among participants with high Alzheimer's disease pathology or gross
 infarcts. Discussion: High CR indicator is associated with preserved
 global cognitive function, episodic memory, and working memory, even in
 the presence of brain pathologies. Our findings highlight the
 important role of high CR accumulation in the prevention of cognitive
 decline.
DOI: 10.25338/b8ns7z
title: Organizational structure and institutional types of community water systems in California

description: Dataset accompanying Dobbin & Fencl (2021) publication entitled
 "Institutional diversity and safe drinking water provision in the
 United States" including secondary data from the U.S. EPA
 and California State Water Resources Control Board as well as the
 author-produced 26-type organizational structural and
 institutional coding of Community Water Systems in California. 
description: See Dobbin & Fencl (2021) (main article body and
 Supplemental Information) and data readme file.
DOI: 10.5061/dryad.3n5tb2rhf
title: Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models

description: Modern phylogenetic comparative methods allow estimating evolutionary
 rates of phenotypic change, how these rates differ across clades, and
 assessing whether the rate remained constant over time. Unfortunately,
 currently available phylogenetic comparative tools express the rate in
 terms of a scalar dimension, hence they do not allow us to determine rate
 variations among different parts of a single, complex phenotype, or
 charting of realized rate variation directly onto the phenotype. Herein,
 we present a new method which allows the mapping of evolutionary rate
 variation directly on three-dimensional phenotypes, informing on the
 direction and magnitude of trait change automatically. This new method,
 implemented by the function rate.map embedded in the R package ‘RRphylo’,
 is based on phylogenetic ridge regression rate estimates. Since the latter
 represent ridge regression slopes, they possess sign and magnitude. In
 ‘RRphylo’, different rates are calculated for different districts of the
 phenotype, which can then be visualized directly onto the phenotype
 itself. We present the application of rate.map to the evolution of facial
 skeleton in Hominoidea (the clade including living and fossil apes), the
 primate clade inclusive of Homo and the greater apes. We found that the
 highly derived, unique shape of the face in modern humans evolved through
 rapid phenotypic changes affecting the nasal bones, the brow ridge and the
 maxillary region. The canine fossa, a facial feature unique to Homo
 sapiens, did not belong to a region of rapid phenotypic change, and could
 be seen as the by-product of midface evolution as suggested by previous
 studies.
DOI: 10.5061/dryad.sf7m0cg6b
title: Data from: Ground and stem sampling as potential detection tools for the wool of Adelges tsugae (Hemiptera: Adelgidae)

description: The wool of the invasive, non-native hemlock woolly adelgid, Adelges
 tsugae Annand (Hemiptera: Adelgidae), occurs mostly on hemlock (Tsuga sp.)
 twigs, but can be dislodged from the canopy and end up on the forest floor
 and tree stem underneath the canopy. Herein, we developed and tested the
 efficacy of two novel sampling techniques, which are based on a visual
 examination of the forest floor and the hemlock stem for A. tsugae wool.
 Subsequently, we compared these two techniques to a visual examination of
 foliage and ball sampling which are two methods currently used
 operationally. We sampled 11 hemlock stands, with low to moderate
 incidence A. tsugae populations, near Ithaca, New York in 2016 and
 assessed the probability of detecting wool on a tree and in a stand, as
 well as the relative variation and relative net precision for each of the
 four techniques. We found that sampling the tree stem outperformed foliage
 and ground sampling, likely because of its higher detection rate and lower
 relative variation, but not ball sampling. Our findings suggest that
 combining stem, ball and ground sampling was the most effective
 combination of techniques and gave a high probability of detecting an
 infested tree or an infested stand. All techniques were an improvement
 over foliage sampling, even after increasing the foliage sampling effort
 fivefold.
description: Data collected using different survey methods for the hemlock
 wooly adelgid. Data were collected from infested stands in New York state
 in 2016. Raw data is provided as is code to produce all the analyses and
 figures presented in the associated paper.
description: Comments are provided in the R code. An up-to-date version of R
 is required. Some additional libraries may be required.