cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6hdr7sr0f
title: Effect of productivity on community size explains the latitudinal diversity gradient of South American small mammals

description: Although many studies have shown that species richness increases from high
 to low latitudes (the latitudinal diversity gradient), the mechanisms
 responsible for generating and maintaining higher species richness in the
 tropics remain intensely debated. Here, we investigate how the effects of
 temperature on speciation rates (kinetic effects) and the effects of
 productivity on community size (chemical effects) explain the latitudinal
 diversity gradient of South American small mammals. We implemented
 Bayesian models that integrate processes from the neutral and metabolic
 theories, comparing model predictions with empirical richness patterns.
 The neutral-metabolic model predicted the latitudinal richness gradient in
 South American small mammals. We found evidence that the effects of
 productivity on community size are more important for explaining
 differences in species richness than the effects of temperature on
 speciation rates. These results suggest that differences in species
 richness along latitudinal gradients are primarily regulated by the
 chemical effects of productivity on speciation-extinction dynamics.
description: <strong>Zip archive of data files</strong> This dataset contains all the files used to investigate how the effects of temperature on speciation rates (kinetic effects) and the effects of productivity on community size (chemical effects) explain the latitudinal diversity gradient of South American small mammals. The data includes 1) grid cell ID, latitude and longitude coordinates, annual mean temperature (temp), net primary productivity (npp), and community data (presence/absence matrix) obtained for the three groups (named files <em>"AllData_Didelphid"</em>, <em>"AllData_Caviomorph"</em>, <em>"AllData_Cricetid"</em>); 2) codes and functions used to perform the neutral-metabolic model and produce the figures presented in the manuscript (named file <em>"Neutral_Metabolic_Model.R"</em>); 3) a South America shapefile (named file <em>"South_America_shapefile"</em>).
DOI: 10.5061/dryad.c866t1g64
title: 12 nuclear microsatellite loci scores for 543 adult trees of Tilia cordata in Lithuainia

description: Genetic signature of the natural genepool of Tilia cordata Mill. in
 Lithuania: compound evolutionary and anthropogenic effects Tilia cordata
 Mill. is a valuable tree species enriching the ecological values of the
 coniferous dominated boreal forests in Europe. Following the historical
 decline, spreading of Tilia sp. is challenged by the elevated inbreeding
 and habitat fragmentation. We studied the geographical distribution of
 genetic diversity of Tilia cordata populations in Lithuania. We used 14
 genomic microsatellite markers to genotype 543 individuals from 23 wild
 growing populations. We found that Tilia cordata retained high levels of
 genetic diversity (population Fis = 0 to 0.15, Ho = 0.53 to 0.69, He =
 0.56 to 0.75). AMOVA, Bayesian clustering and Monmonier’s barrier
 detection indicate weak but significant differentiation among the
 populations (Fst = 0.037***) into geographically interpretable clusters of
 (a) western Lithuania with high genetic heterogeneity but low genetic
 diversity, bottleneck effects, (b) relatively higher genetic diversity of
 Tilia cordata on rich and most soils of midland lowland, and (c) the most
 differentiated populations on poor soils of the coolest north-eastern
 highland possessing the highest rare allele frequency but elevated
 inbreeding and bottleneck effects. Weak genetic differentiation among the
 Tilia cordata populations in Lithuania implies common ancestry, absence of
 strong adaptive gradients and effective genetic exchange possible mediated
 via the riparian networks. A hypothesis on riparian networks as geneflow
 mediators in Tilia cordata was raised based on results of this study.
description: DNA samples were collected from 543 adult trees in ca. 20
 populations of presumably natural origin in Lithuiania. 12 nuclear SSR
 loci were scored with ABI DNA sequencer. 
description: Data is ready for runing in GeneAlex (Exlcel format) with
 parameters already set. The last three columns are lat long and region of
 orgin.
DOI: 10.5061/dryad.83bk3j9qz
title: Tolerance niche expansion and potential distribution prediction during Asian openbill bird range expansion

description: It is prevalent to use ecological niche models in the analysis of species
 expansion and niche changes. However, it is difficult to estimate the
 niche when alien species fail to establish in exotic areas. Here, we
 applied the tolerance niche concept, which means that niche of species can
 live and grow but preclude a species from establishing self-sustaining
 populations, in such fail-to-establish events. Taking the rapidly expanded
 bird, Asian openbill (Anastomus oscitans), as a model species, we
 investigated niche dynamics and its potential effects on the population by
 Niche A and ecospat, predicted potential distribution by biomod2. Results
 showed that niche expansion has occurred in two non-native populations
 caused by the tolerance of colder and wetter environments, and potential
 distribution mainly concentrated on equatorial islands. Our study
 suggested that the expanded niche belongs to tolerance niche concept
 according to the populations' dynamics and GPS tracking evidence. It
 is essential to consider source populations when we analyse the alien
 species. We recommended more consideration to the application of tolerance
 niche in alien species research, and there is still a need for standard
 measurement frameworks for analysing the tolerance niche.
DOI: 10.7291/d1n38k
title: Burrowing crabs and physical factors hasten marsh recovery at panne edges

description: Salt marsh loss is projected to increase as sea-level rise accelerates
 with global climate change. Salt marsh loss occurs along both lateral
 creek and channel edges and in the marsh interior, when pannes expand and
 coalesce. Often, edge loss is attributed to erosive processes whereas
 dieback in the marsh interior is linked to excessive inundation or
 deposition of wrack, but remains poorly understood. We conducted a
 two-year field investigation in a central California estuary to identify
 key factors associated with panne contraction or expansion. Our study
 explored how an abundant burrowing crab, shown to have strong negative
 effects on marsh biomass near creek edges, affects panne dynamics. We also
 explored which physical panne attributes best predicted their dynamics. To
 our knowledge, ours is the first study of panne dynamics in a California
 marsh, despite how ubiquitous pannes are as a feature of marshes in the
 region and how often extensive marsh dieback occurs via panne expansion.
 Overall, we found that pannes contracted during the study period, but with
 variable rates of marsh recovery across pannes. Our model incorporating
 both physical and biological factors explained 86% of the variation in
 panne contraction. The model revealed a positive effect of crab activity,
 sediment accretion, and a composite of depth and elevation on panne
 contraction, and a negative effect of panne size and distance to nearest
 panne. The positive crab effects detected in pannes contrast with negative
 effects we detected near creek edges in a previous study, highlighting the
 context-dependence of top-down and bioturbation effects in marshes. As
 global change continues and the magnitude and frequency of disturbances
 increases, understanding the dynamics of marsh loss in the marsh interior
 as well as creek banks will be critical for the management of these
 coastal habitats.
description: Please see ReadMe sheet within the datafile.
DOI: 10.5061/dryad.q83bk3jhb
title: Changes in measures of cognitive function in patients with end-stage kidney disease on dialysis and the effect of dialysis vintage: A longitudinal cohort study

description: Introduction: Prevalence of cognitive impairment increases with
 worsening severity of chronic kidney disease (CKD) and the majority of
 end-stage kidney disease (ESKD) patients on dialysis have cognitive
 impairment. Trends of cognitive function (CF) in this population are less
 well known with published studies reporting conflicting results.
 Methods: We assessed CF in a cohort of non-dialysis CKD and ESKD
 patients undergoing dialysis using modified mini-mental state examination
 (3MS), trail-making test (TMT-A & B) scores and Stroop task, and
 evaluated demographics, comorbidities, and depression using Beck
 depression inventory at baseline. We repeated tests of CF and
 depression &gt; 1-year after baseline in both groups
 and compared change scores in CF and depression between ESKD/ CKD
 sub-groups. Among ESKD patients we compared change scores between patients
 with dialysis vintage of &lt;1-year and &gt;1-year. Analysis of
 covariance was used to adjust for the effect of age on these change
 scores.  Results:  At baseline (N=211),
 compared to CKD (N=108), ESKD (N=103) patients had significantly worse CF
 based on 3MS and TMT-A & B scores, and depression scores. On
 follow-up (N=160) 3MS scores, especially the memory subscale significantly
 improved in ESKD, but worsened in CKD, with no significant changes in TMT
 A /TMT-B, or depression scores after adjusting for age. Among ESKD
 patients, 3MS, especially memory subscale improved in patients with
 dialysis vintage &lt;1-year compared to &gt;1-year. The 51
 patients who discontinued after baseline assessment had worse baseline CF
 scores suggesting differential attrition.   
 Conclusion: Though baseline cognitive scores were worse in ESKD
 patients on dialysis, compared to CKD, their 3MS, especially memory
 subscale improved on follow-up. Among ESKD patients, the improvement was
 significant only in patients who have been on dialysis for less than one
 year which may indicate a beneficial effect of clearance of uraemic
 toxins. Differential attrition of study subjects may have impacted the
 observed results. 
description: Data were collected by research assistants by patient interviews
 and administering validated test instruments. Data were
 entered into an excel spreadsheet by research assistants.
 The data were analyzed using Stata 16.0.
DOI: 10.5061/dryad.b8gtht7c2
title: Data from: Substantia nigra integrity correlates with sequential working memory in Parkinson’s disease

description: Maintaining and manipulating sequential information online is essential
 for daily activities such as planning. In Parkinson’s disease (PD),
 deficits in sequential working memory have been associated with altered
 regional activation and functional connectivity within the basal ganglia.
 This study demonstrated that the substantia nigra (SN) integrity
 correlates with basal ganglia dysfunction during sequential working
 memory. We included 29 patients with PD and 29 healthy controls (HC). We
 assessed the SN integrity using neuromelanin-sensitive MRI and sequential
 working memory using functional MRI and a digit ordering task. In this
 task, participants either recalled a sequence of digits in the original
 order (‘pure recall’) or rearranged the digits in ascending order and
 recalled the new sequence (‘reorder & recall’). PD showed smaller
 SN areas than HC, especially on the left side. Compared to HC, PD showed
 lower task accuracy, hyper-activation of the subthalamic nucleus,
 hypo-activation of the caudate nucleus and globus pallidus, and weakened
 functional connectivity between the bilateral SN and all three basal
 ganglia regions. Moreover, PD showed distinct brain-behavior and
 structure-function relationships. Ordering-related accuracy cost (‘reorder
 & recall’ versus ‘pure recall’) correlated with the
 ordering-related subthalamic activation in HC, but with the
 ordering-related caudate activation in PD. In PD, the caudate activation
 correlated with the total SN area, whereas the subthalamic activation
 correlated with daily exposure to D2/3 receptor agonists. In conclusion,
 damage to the SN may lead to basal ganglia dysfunction sequential working
 memory deficits even in early PD.
DOI: 10.5061/dryad.qfttdz0gh
title: Slow oscillation-spindle coupling strength predicts real-life gross-motor learning in adolescents and adults

description: Previously, we demonstrated that precise temporal coordination between
 slow oscillations (SO) and sleep spindles indexes declarative memory
 network development (Hahn et al., 2020). However, it is unclear whether
 these findings in the declarative memory domain also apply in the motor
 memory domain. Here, we compared adolescents and adults learning juggling,
 a real-life gross-motor task. We found that improved task proficiency
 after sleep lead to an attenuation of the learning curve, suggesting a
 dynamic juggling learning process. We employed individualized
 cross-frequency coupling analyses to reduce inter and intra-group
 variability of oscillatory features. Advancing our previous findings, we
 identified a more precise SO-spindle coupling in adults compared to
 adolescents. Importantly, coupling precision over motor areas predicted
 overnight changes in task proficiency and learning curve, indicating that
 SO-spindle coupling is sensitive to the dynamic motor learning process.
 Our results provide first evidence that regionally specific precisely
 coupled sleep oscillations support gross-motor learning.
DOI: 10.5061/dryad.kprr4xh45
title: Phylogeny and time scale of diversification in the fossil-rich Sunfishes and Black Basses (Teleostei: Percomorpha: Centrarchidae)

description: Species of the North American freshwater fish lineage Centrarchidae are
 apex predators in their habitats and are among the world’s most popular
 sport fishes. Centrarchids boast a rich fossil record that extends from
 the latest Eocene to the Pleistocene. To investigate the phylogeny and
 timing of diversification of Centrarchidae, we deploy a dataset of DNA
 sequences of 16 nuclear genes sampled from nearly all of the recognized
 and undescribed species. We also utilize previously published
 morphological datasets to assess the phylogenetic placement of one of the
 oldest known centrarchid fossils, †Plioplarchus whitei. A Bayesian
 multispecies coalescent species tree analysis provides insight on
 relationships that evaded resolution in earlier studies, such as the
 relationships of Acantharchus pomotis, the resolution of a clade
 consisting of species previously synonymized under the Spotted Bass,
 Micropterus punctulatus, and a clade of recently described species
 previously considered populations of the Redeye Bass, Micropterus coosae.
 This new molecular phylogeny and the inclusion of †P. whitei and other
 centrarchid fossils in the tip-dated fossilized birth-death analysis
 results in a new hypothesis of the timing of diversification in
 Centrarchidae that contextualizes the ages of centrarchid fossils to the
 timing of speciation among the extant species. In addition to providing
 new temporal perspectives on the diversification of freshwater fishes in
 North America, this study may close of the chapter of centrarchid
 phylogeny inferred using Sanger sequenced genes, as the use of
 genomic-scale datasets becomes mainstream in the phylogenetics of fishes.
description: Sanger DNA sequencing of single copy nuclear genes.
DOI: 10.5061/dryad.j3tx95xd5
title: Data from: Exotic tree plantations as alternative breeding habitat for an endemic avian predator

description: This dataset contains information on breeding habitat and breeding
 parameters for an island endemic raptor, the
 Macaronesian sparrowhawk Accipiter nisus granti, on Tenerife,
 Canary Islands, during the breeding seasons of 2014 and 2015.
 Breeding territories are distributed in three
 main forest types, two natives (laurel forest and Canarian
 pinewood) and one composed of exotic trees. We provide the
 following breeding parameters: a) breeding success as the percentage of
 occupied nests that produced fledglings; b) productivity as the average
 number of fledglings produced per nest; and c) brood size as the average
 number of fledglings produced per successful nest. The dataset
 contains nesting habitat variables at macro-, micro-habitat, and nest tree
 levels. We also provide information on the survival of nest structures.
description: The dataset was collected during March-August of 2014 and 2015 on
 Tenerife, Canary Islands. Data have been processed by a series of
 generalized linear models and generalized linear mixed models to produce a
 manuscript accepted for publication in <em>Journal of Avian
 Biology</em> (see details in
 https://doi.org/10.1111/jav.02527).
DOI: 10.15468/dl.hjzyyr
title: Occurrence Download

description: A dataset containing 121807 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pachydiplax longipennis"
 ]
}

 The dataset includes 121807 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002806-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x69p8czhh
title: Green leaf phenological characteristics of boreal peatland vegetation impacted by linear disturbances

description: Vast areas of boreal peatlands are impacted by linear disturbances known
 as seismic lines. Tree removal and ground disturbance alter vegetation
 communities and are expected to change ecosystem functioning. As boreal
 landscapes continue to be disturbed by linear disturbances, understanding
 the magnitude and mechanisms of vegetation and phenology changes is the
 first step toward predicting carbon cycling changes across broad spatial
 scales. We investigate seismic line disturbances on peatland plant
 community composition and phenological patterns using readily available
 digital photography at a bog and a fen in Alberta, Canada. Our objectives
 were to: 1) compare the understory peatland vegetation on seismic lines
 with those in adjacent undisturbed areas using two phenological metrics
 (green and red chromatic coordinates); 2) evaluate if vegetation greenness
 is directly related to vegetation community composition, and 3) determine
 whether plot-scale greenness predicts plant productivity. We found that
 areas of peatlands intersected by seismic lines have an earlier seasonal
 peak (maximum greenness) compared to undisturbed areas, and vegetation
 communities had a stronger relationship to greenness and gross primary
 production (GPP) at disturbed areas relative to undisturbed areas. This
 change in understory vegetation results in greater CO2 uptake in disturbed
 areas. We demonstrate an easy-to-use application of digital photography
 that successfully quantifies phenological changes in boreal peatland
 vegetation. This non-destructive method for understanding vegetation
 phenology eliminated the need for fixed infrastructure and allowed us to
 expand our sampling capacity and study sites while allowing for repeated
 measures in the future.
DOI: 10.5061/dryad.ghx3ffbnk
title: Data for: Comparative thermal performance among four young-of-the-year temperate reef fish species

description: Identifying the role of temperature on species-specific performance is
 critical for predicting how species will  respond to temperature
 increases expected under climate change. We compared thermal performance
 of two sympatric Pacific rockfish species complexes (controls for
 relatedness and geographic location) that vary in larval life-history
 traits associated with different oceanographic regimes including
 temperature during early life-history stages: the BY complex (Black:
 Sebastes melanops, Yellowtail: S. flavidus) and the CQ complex (Copper: S.
 caurinus, Quillback: S. maliger). By using controlled 
 experiments, we evaluated foraging activity, growth and survival of
 young-of-the-year (YOY) rockfish recruits under current and future habitat
 temperatures over a 14-day time period indicative of marine heatwave
 events expected with climate change. BY rockfish displayed a
 heat-intolerant behavior by only foraging at temperatures within current
 habitat temperatures, whereas the CQ rockfish displayed a heat-tolerant
 behavior by actively foraging at temperatures above current and future
 predicted temperatures for a limited time. Although growth and survival in
 each species significantly declined with temperature, the magnitude of the
 effect did not vary between species. Taken together, our results show that
 rockfish are capable of using different behavioral strategies to cope with
 warming, and may be differentially impacted by future climate conditions.
description: All data files, R scripts and raw image and video files are
 provided in this zip file. Fish images that were used for a measurement
 are recorded in the Photo_Name column of the Fish_Measurement_Data_File.
 All videos for identifying foraging activity rates are provided. All
 videos were watched by two viewers and scored twice by each viewer and
 those data are provided in 20171129_AcivityData file.
DOI: 10.5061/dryad.gmsbcc2mw
title: Links between personality traits and problem-solving performance in zebra finches (Taeniopygia guttata)

description: Consistent individual differences in behaviour across time or contexts
 (i.e., personality types) have been found in many species and have
 implications for fitness. Likewise, individual variation in cognitive
 abilities has been shown to impact fitness. Cognition and personality are
 complex, multidimensional traits. However, previous work has generally
 examined the connection between a single personality trait and a single
 cognitive ability, yielding equivocal results. Links between personality
 and cognitive ability suggest that behavioural traits coevolved and
 highlight their nuanced connections. Here we examined individuals’
 performance on multiple personality tests and repeated problem-solving
 tests (each measuring innovative performance). We assessed behavioural
 traits (dominance, boldness, activity, risk-taking, aggressiveness, and
 obstinacy) in 41 captive zebra finches. Birds’ scores for boldness and
 obstinacy were consistent over two years. We also examined whether
 personality correlated with problem-solving performance on repeated tests.
 Our results indicate that neophobia, dominance, and obstinacy were related
 to successful solving, and less dominant, more obstinate birds solved the
 tasks quicker on average. Our results indicate the importance of examining
 multiple measures over a long period. Future work that identifies links
 between personality and innovation in non-model organisms may 
 elucidate the coevolution of these two forms of individual differences.