cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h7kn8
title: Data from: Delusion-proneness displays comorbidity with traits of autistic-spectrum disorders and ADHD

description: There is an increasing body of evidence suggesting a significant
 comorbidity between psychotic disorders such as schizophrenia and
 attention-deficit/hyperactivity disorder (ADHD) or autism-spectrum
 disorders (ASD). Recently, research on psychosis-proneness in otherwise
 healthy individuals has been a promising way to better understand the
 mechanisms underlying psychosis. As both ADHD and ASD symptoms show a
 normal distribution in the general population, such trait comorbidity may
 confound studies on psychosis-proneness. Thus, understanding the extent to
 which psychosis-proneness relates to ADHD and ASD symptoms in healthy
 subjects is crucial for studies focusing on at-risk or psychosis-prone
 populations. In the present paper we tested the robustness of overlap
 between psychosis-proneness and ADHD/ASD symptoms, by studying
 correlations between the scores of three commonly-used questionnaires
 assessing delusion-proneness (Peters’ Delusion Inventory), ADHD tendencies
 (Adult ADHD Self-Report Scale) and ASD tendencies (Autism Quotient), on a
 large sample of healthy individuals (n=925) using raw scores, prototypical
 questions and a factor analysis. The results showed consistently positive
 correlations between psychosis-proneness and ADHD-, as well as
 ASD-symptoms. While the effect was weak for ASD, it was moderate for ADHD.
 The findings support the idea that when investigating psychosis-proneness
 it is crucial to also take ADHD- and ASD-tendencies into account, in order
 to conclude that the reported results in a given study are specific to
 psychosis-proneness. The observed trait correlations also suggest a common
 pathway in the underlying information processing of these states.
description: Answers to AQ, ASRS, PDI
 questionnairesThis Excel file contains
 the answers to every item of each of the 3 questionnaires (AQ, ASRS, PDI),
 for all the participants (n=925). This is the raw data, so no score has
 been computed. The answers of each questionnaire are presented separately,
 on individual spreadsheets (3 in total). The questionnaire items are also
 presented on individual spreadsheets (3 in total).data_full_questionnaires_AQ_ASRS_PDI.xlsx
DOI: 10.5061/dryad.h26v5
title: Data from: In and out of refugia: historical patterns of diversity and demography in the North American Caesar’s mushroom species complex

description: Some of the effects of past climate dynamics on plant and animal diversity
 make-up have been relatively well studied, but to less extent in fungi.
 Pleistocene refugia are thought to harbor high biological diversity (i.e.
 phylogenetic lineages and genetic diversity), mainly as a product of
 increased reproductive isolation and allele conservation. In addition,
 high extinction rates and genetic erosion is expected in previously
 glaciated regions. Some of the consequences of past climate dynamics might
 involve changes in range and population size that can result in divergence
 and incipient or cryptic speciation. Many of these dynamic processes and
 patterns can be inferred through phylogenetic and coalescent methods. In
 this study, we first delimit species within a group of closely related
 edible ectomycorrhizal Amanita from North America (the American
 Caesar's mushrooms species complex) using multi-locus
 coalescent-based approaches; and then address questions related to effects
 of Pleistocene climate change on the diversity and genetics of the group.
 Our study includes extensive geographic sampling throughout the
 distribution range, and DNA sequences from three nuclear protein-coding
 genes. Results reveal cryptic diversity and high speciation rates in
 refugia. Population sizes and expansions seem to be larger at mid-range
 latitudes (Mexican highlands and SE USA). Range shifts are proportional to
 population size expansions, which were overall more common during the
 Pleistocene. This study documents responses to past climate change in
 fungi, and also highlights the applicability of the multi-species
 coalescent in comparative phylogeographic analyses and diversity
 assessments that include ancestral species.
description: Basic
 dataThis zip files contains
 six directories, each one includes basic data used for analyses. The
 "alignments" directory includes concatenated, phased, and
 unphased gene alignments. The "trees" directory includes MCC
 tree files in nexus format, produced by BEAST and starBEAST. Trees include
 individual gene trees, concatenated, and species trees. The
 "bpp" folder includes the control, tree, and imap files needed
 to run BP&P. The "maxent_input" folder has the filtered
 input coordinates used to run maxent in R. The "asr_div_data"
 has the geographic states used in RASP and data for MuSSE in a RData file.
 Finally, the "popsize_data" includes a table with summarized
 information about extant and ancestral population sizes and
 latitudes.Dryad.zip
DOI: 10.5061/dryad.1t67j57q
title: Data from: Phylogeography of the catfish Hatcheria macraei reveals a negligible role of drainage divides in structuring populations

description: Southern South America provides a set of unusual geographic features that
 make it particularly interesting for studying phylogeography. The Andes
 Mountains run along a north-to-south axis and act as a barrier to gene
 flow for much of the biota of this region, with southern portions
 experiencing extensive historic glaciation. Geological data reveal a
 series of drainage reversals, shifting from Pacific Ocean outlets to
 Atlantic Ocean outlets due to glacier formation that dammed and reversed
 rivers. Once glaciers melted around 13 000 years ago, drainages returned
 to the Pacific Ocean. This geologic history predicts that aquatic
 organisms in Pacific rivers should have their closest relationships to
 their counterparts in Atlantic rivers immediately to their east. We tested
 this prediction in the trichomycterid catfish Hatcheria macraei from 38
 locations using the mitochondrial cytochrome b gene. Our results show that
 most populations found in Pacific rivers were closely related to fish
 found in the adjacent Atlantic draining Río Chubut. Surprisingly, one
 documented drainage reversal (from Río Deseado into Río Baker) did not
 result in movement of H. macraei. Overall, we found the lowest levels of
 genetic structure between most Pacific rivers that are adjacent to the
 Atlantic draining Río Chubut. We also found low levels of population
 structuring among three out of four river basins that drain to the
 Atlantic Ocean. Our findings suggest that drainage basin boundaries have
 historically not played an important long-term role in structuring between
 nine out of 11 drainages, an unusual finding in freshwater biogeography.
description: All Hatcheria Cytb
 sequences, plus outgroupsFasta file containing
 all of the Cytochrome b sequences for Hatcheria macraei, plus outgroup
 samples. Unique haplotypes are labeled with the haplotype number preceding
 the isolate label. The isolate label usually consists of the initials of
 the species (HM, TA) followed by the first four letters of the locality.
 See readme file for which codes are associated with specific
 populations.hatch.cytb.all.individuals2.fasArlequin Analysis file for all Hatcheria Cytb sequences grouped by populationArlequin file, individuals were first grouped by population in DNAsp, then grouped by river drainage in Arlequinhatch.by.pop.arpArlequin analysis file that contains all Hatcheria Cytb haplotypesArlequin haplotype file output from DNAsp. Place this file in the same directory as the Arlequin project file.hatch.by.pop.hapRAxML datafile for all Hatcheria haplotypes plus outgroupsDatafile used in our phylogenetic analyses. Labels consist of the haplotype number and isolate name.hatch.cytb.haps.phy
DOI: 10.5061/dryad.nq8nd
title: Data from: An investigation on Mycetinis (Euagarics; Basidiomycota)

description: Molecular analyses have revealed a clade which equates with the genus name
 Mycetinis Earle. An overall survey of this genus, however, has not been
 forthcoming. The current study summarizes taxa which are placed in
 Mycetinis based on morphological and/or molecular data. Fifteen taxa are
 accepted: Mycetinis scorodonius f. diminutivus and Mycetinis yunnanensis
 are proposed as new, while Mycetinis cinnamomeus, Mycetinis olidus,
 Mycetinis prasiosmus, Mycetinis subalpinus and Myctinis virgultorum are
 newly recombined binomials. Phylogenies based on molecular data show
 overall disposition in Omphalotaceae, Gymnopus and allied genera, and taxa
 of Mycetinis.
description: ML tree of mycetinis
 Figure2PhyML tree of Mycetinis
 based on ITS sequences showing relationships within Mycetinis and between
 Mycetinis and Gymnopus taxaML tree of
 scorodonius_ITS Figure 77Unrooted PhyML tree
 based on Mycetinis scorodonius ITS sequences.
DOI: 10.5061/dryad.6n0m8
title: Data from: A superlinear iteration method for calculation of finite length journal bearing's static equilibrium position

description: Solving the static equilibrium position is one of the most important parts
 of dynamic coefficients calculation and further coupled calculation of
 rotor system. The main contribution of this study is testing the
 superlinear iteration convergence method - twofold secant method, for
 determination of the static equilibrium position of journal bearing with
 finite length. Essentially, the Reynolds equation for stable motion is
 solved by finite difference method and the inner pressure is obtained by
 successive over-relaxation iterative method reinforced by the compound
 Simpson quadrature formula. The accuracy and efficiency of the twofold
 secant method are higher in comparison with the secant method and
 dichotomy. The total number of iterative steps required for the twofold
 secant method are about one-third of secant method and less than
 one-eighth of dichotomy for the same equilibrium position. The
 calculations for equilibrium position and pressure distribution for
 different bearing length, clearance and rotating speed were done. In the
 results, the eccentricity presents linear inverse proportional
 relationship to the attitude angle. The influence of the bearing length,
 clearance and bearing radius on the load-carrying capacity were also
 investigated. The results illustrate that larger bearing length, larger
 radius and smaller clearance are good for the load-carrying capacity of
 journal bearing. The application of twofold secant method can greatly
 reduce the computational time for calculation of the dynamic coefficients
 and dynamic characteristics of rotor-bearing system with a journal bearing
 of finite length.
description: Data from figure 5 to
 figure 16Data form figure 5 to figure
 16.rar
DOI: 10.5061/dryad.hq347
title: Data from: Selection at the Esterase-2 locus of Drosophila buzzatii? Perturbation-reperturbation experiments

description: Apparent selection affecting starch gel electrophoretic alleles at the
 Esterase-2 locus of Drosophila buzzatii has been detected in laboratory
 and natural populations. Perturbation-reperturbation of allele frequencies
 in replicated laboratory populations attempts to test direct selective
 effects at the locus versus effects of linked loci. Sequential gel
 electrophoresis has identified more alleles within starch classes, and
 three of these alleles (within the a, b and c starch alleles) were used in
 cage population experiments. Allele a/1.00/1.00/1.00 was set up in 10
 replicate populations with allele c/1.00/1.00/1.00, and in an independent
 10 replicate populations with allele b/0.99/1.01/1.00. For each set, three
 reperturbations were done. Replicate populations generally showed similar
 patterns of allele frequency change and clear directionality: effects of
 selection, not drift. However, four populations deviated from their
 replicates, indicating dissipation of linkage disequilibrium. Estimates of
 pre-adult viability in the F2 of pair-wise crosses among 12 sequential gel
 electrophoretic alleles showed very variable modes of inheritance and
 relative viability fitnesses. Together with the diversity of patterns of
 allele frequency change in the cage populations, these results suggest a
 gene complex, with selection acting on an interacting set of loci which
 may include Esterase-2.
description: IT6_IH13_DATA - Cages
 1-10 and associated reperturbation (R) cagesAllele frequency results
 for the initial perturbation and reperturbation cages -
 IT6_IH13IT6_IH13_DATA.xlsIT6_IT15_DATA - Cages 11-20 and associated reperturbation (R) cagesIT6_IT15_DATA.xlsEst fitness crossesResults of all pairwise crosses - F2 genotype counts and chi square tests for fit to 1:2:1 ratio.
DOI: 10.5061/dryad.66h3627
title: Data from: Diversity patterns in Upper Cambrian to Lower Ordovician trilobite communities of north-western Argentina

description: The hierarchical structure of biodiversity from a regional scale analysis
 has received much attention as an alternative approach to unravelling the
 principal drivers of biodiversification. To better understand the
 processes that control the diversification of Cambro‐Ordovician trilobite
 communities from the Argentine Cordillera Oriental, we explore patterns of
 occupancy and diversity trajectories at the local and regional scales
 through seven intervals (Furongian, loTr1, upTr1, loTr2, upTr2, Tr3 and
 Fl2–3), and across an onshore‐offshore profile. Our results indicate: (1)
 a decrease in regional diversity from the upper Tr2 onwards, mainly caused
 by a reduction in the number of rare taxa, coupled with stable beta
 diversity at regional scale and a constant rise in beta diversity in deep
 subtidal environments; (2) a higher proportion of regional diversity
 allocated to the within‐habitat beta component; and (3) that changes in
 gamma diversity are driven primarily by changes in alpha diversity during
 the Furongian–Tr3, whereas in the Floian, beta diversity seems to modulate
 regional diversity. These trends and associated patterns indicate
 increasing ecological differences among taxa, shifting from
 metacommunities where most taxa have similar ecological preferences or
 ‘Hubbell type’ to metacommunities with high niche differentiation or
 ‘Hutchinson type’. Interestingly, the timing of this shift coincides with
 the regional‐scale turnover between trilobite evolutionary faunas
 suggesting that the rise in niche differentiation among these genera may
 be related to the transition. Superimposed on this general trend,
 particular diversity structures can be understood in the light of
 metacommunity dynamics, such as dispersal limitation and mass effect.
description: Trilobite occurrence
 datasetTrilobite
 presence-absence dataset of samples from the Cambro-Ordovician of the
 Argentine Cordillera Oriental with environmental assignation (shallow
 subtidal, deep subtidal, offshore).Dataset.xlsR codeR code for the diversity analysesList of generaNames of the genera corresponding to the numbers that appear in the occupancy-rank plots depicted in figure 4.list of taxa.xls
DOI: 10.5061/dryad.rd912
title: Data from: A 37-year experimental study of effects of structural alterations on a shrub community in the Mojave Desert, California

description: 1. In 1977 an experiment was initiated in the Mojave Desert to investigate
 how shrub interactions affect structure in a community dominated by
 Ambrosia dumosa and Larrea tridentata. Here, as in much of the Mojave,
 Larrea were regularly distributed, Ambrosia occurred in aggregations, and
 the two were randomly distributed relative to each other. Pre-dawn xylem
 pressure potentials (PDXPPs) of single Ambrosia or Larrea in centers of
 100m2 circular plots were monitored to assess effects of intraspecific,
 interspecific, and total removals of neighboring shrubs. Contrary to
 theory, results over the next two years indicated interspecific
 interference was more intense than intraspecific interference in both
 species. 2. These plots were maintained through 2014. Measurements of
 seedling recruitment from 1980 to 2014, and of PDXPP, aboveground biomass,
 and canopy senescence from 2003 to 2014 were conducted. 3. Recruitment of
 both species was substantial immediately after the removals, but declined
 to very low levels after 1983. Ambrosia recruited into all Ambrosia and
 Total-Removal plots, but Larrea recruited only into plots that contained
 mature Ambrosia. 4. PDXPPs of monitored shrubs continued to be enhanced in
 removal plots for at least 27 years, but this changed from most being due
 to interspecific removals in both species to intraspecific removals
 causing most enhancement in Ambrosia and inter- and intraspecific removals
 causing nearly equal enhancements in Larrea. 5. Aboveground biomasses of
 monitored shrubs of Ambrosia and Larrea were 2.1X and 2.8X larger in
 Total-Removal plots, 1.6X and 1.7X larger in intraspecific removal plots,
 respectively, and 1.1X larger in interspecific removal plots for both
 species than those in Control plots, indicating the absence of
 intraspecific interference had the dominant long-term effect. 6. Canopy
 senescence differed between Ambrosia and Larrea in extent, timing and
 effect of specific removal treatments; it was greatest for both species in
 Controls, averaging 75% and 34%, respectively. 7. Synthesis. Shrub
 interactions and their relations to community structure are
 mechanistically and spatially complex. Differences between short-term and
 long-term responses to removals reveal multi-tiered, temporally dynamic
 feedback loops between shrub interactions and community structure driven
 by demographics, species-specific root growth, resource competition,
 communications, and territoriality.
description: LTDS - Ambrosia PDXPP
 data archivesee
 publicationLTDS - Ambrosia plots,
 Removal records archivesee
 publicationLTDS - Ambrosia size
 data archivesee
 publicationLTDS - KEY for plots and
 treatmentssee
 publicationLTDS - Larrea PDXPP data
 archivesee
 publicationLTDS - Larrea plots,
 Removal records, data archivesee
 publicationLTDS Larrea size data
 archivesee
 publicationLTDS Rainfall data
 archivesee
 publication
DOI: 10.5061/dryad.00nd1
title: Data from: The evolution of age-dependent plasticity

description: When organisms encounter environments that are heterogeneous in time,
 phenotypic plasticity is often favored by selection. The degree of such
 plasticity can vary during an organism’s lifetime, but the factors
 promoting differential plastic responses at different ages or life stages
 remain poorly understood. Here we develop and analyze an evolutionary
 model to investigate how environmental information is optimally collected
 and translated into phenotypic adjustments at different ages. We
 demonstrate that plasticity must often be expected to vary with age in a
 nonmonotonic fashion. Early in life, it is generally optimal to delay
 phenotypic adjustments until sufficient information has been collected
 about the state of the environment to warrant a costly phenotypic
 adjustment. Toward the end of life, phenotypic adjustments are disfavored
 as well because their beneficial effects can no longer be fully reaped
 before death. Our analysis clarifies how patterns of age-dependent
 plasticity are shaped by the interplay of environmental uncertainty, the
 accuracy of perceived information, and the costs of phenotypic adjustments
 with life-history determinants such as the relative strengths of fecundity
 and viability selection experienced by the organism over its lifetime. We
 conclude by comparing our results with expectations for alternative
 mechanisms, including developmental constraints, that promote
 age-dependent plasticity.
description: AgeDependentPlasticity.cppC++ source code for finding the optimal reaction norm for age-dependent plasticity. The compiled program executes a backward state-dependent optimization procedure, as outlined in our paper.makeGraphs.nbThis Mathematica notebook (created using Mathematica version 8.0) can be used to create phenotype and estimate trees, as well as plots of the optimal reaction norm from the output files generated by the optimization program.
DOI: 10.5061/dryad.vb25b35j
title: Data from: Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography

description: AIM: Palms (Arecaceae/Palmae) are a model group for evolutionary studies
 in the tropics. Family-wide data on taxonomy, phylogenetics and
 distribution are now available, but a general framework of palm evolution
 is still lacking. The overall aim of this study, published in two
 companion papers, is to seek evolutionary explanations for the
 geographical distribution of palm lineages and species diversity patterns
 at global and regional levels. In this first paper we undertake a detailed
 analysis of palm biogeography for all major lineages in a global context,
 comparing our results to the fossil record, molecular dating studies and
 previously established biogeographical hypotheses for the family.
 LOCATION: Global. METHODS: A dated phylogeny of all palm genera and
 distributional data were used to infer ancestral areas. A global model of
 area evolution for tropical lineages was formulated and ancestral areas
 were reconstructed using a maximum likelihood approach under the
 dispersal–extinction–cladogenesis model. RESULTS: The crown node
 divergence of palms and divergences of all five subfamilies occurred
 before the end of the Cretaceous within Laurasian regions. Early range
 expansions into South America took place in the stem lineages of
 subfamilies Arecoideae and Ceroxyloideae, and into Africa and South
 America in Cretaceous lineages within subfamily Calamoideae. The largest
 subfamily Arecoideae underwent its early diversification history in South
 America and has been an important source of lineages expanding into other
 regions, notably in the major Indo-Pacific tribe Areceae. In contrast, the
 history of subfamily Coryphoideae was primarily Laurasian, supporting
 earlier boreotropical hypotheses for the group. Dispersals across
 Wallace's Line are prevalent in major groups of Arecoideae,
 Calamoideae and Coryphoideae, both before and after the Miocene geological
 evolution of the Malesian Archipelago. MAIN CONCLUSIONS: We present the
 first robust biogeographical hypothesis for the evolution of palms in
 space and time. Although palms show evidence of dispersal limitation, our
 findings highlight the role of long-distance dispersal events in the
 establishment of major biogeographical patterns of palm clades. This is
 consistent with the growing evidence for long-distance dispersal as a
 major mechanism underpinning the distribution of tropical lineages.
description: Baker and Couvreur palm
 chronogramComplete genus-level
 chronogram of the palm family (Arecaceae/Palmae). Open using FigTree
 http://tree.bio.ed.ac.uk/software/figtree/Baker & Couvreur_raw
 Lagrange outputA raw text output from a
 Dispersal-Extinction-Cladogenesis (DEC) analysis conducted using Lagrange.
 Saved as a Word .doc file. Additional formats added by Dryad
 staff.