cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4cj4k
title: Data from: Experiments and modelling of rate-dependent transition delay in a stochastic subcritical bifurcation

description: Complex systems exhibiting critical transitions when one of their
 governing parameters varies are ubiquitous in nature and in engineering
 applications. Despite a vast literature focusing on this topic, there are
 few studies dealing with the effect of the rate of change of the
 bifurcation parameter on the tipping points. In this work, we consider a
 subcritical stochastic Hopf bifurcation under two scenarios: the
 bifurcation parameter is first changed in a quasi-steady manner and then,
 with a finite ramping rate. In the latter case, a rate-dependent
 bifurcation delay is observed and exemplified experimentally using a
 thermoacoustic instability in a combustion chamber. This delay increases
 with the rate of change. This leads to a state transition of larger
 amplitude compared to the one that would be experienced by the system with
 a quasi-steady change of the parameter. We also bring experimental
 evidence of a dynamic hysteresis caused by the bifurcation delay when the
 parameter is ramped back. A surrogate model is derived in order to predict
 the statistic of these delays and to scrutinise the underlying stochastic
 dynamics. Our study highlights the dramatic influence of a finite rate of
 change of bifurcation parameters upon tipping points and it pinpoints the
 crucial need of considering this effect when investigating critical
 transitions.
description: Experimental time
 tracesSets of acoustic
 measurements of the thermoacoustic subcritical bifurcation recorded from
 our lab-scale swirled-flame combustor. The files 2016-10-20_StationaryX
 are the long time traces recorded at stationary conditions at 7 different
 operative points, the files 2016-10-20_Ramp1Y are different sections of an
 experiment performed ramping the operative condition over
 time.Experimental_time_traces_tdms.zip
DOI: 10.5064/f6vanjl8/igtb9m
title: Silan-Ciruelas_FRA_Opt1_8A_1_5_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/i8zeth
title: Silan-Ciruelas_TUR_Opt1_6A_EdaDamla_1-5_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/3nn9oe
title: Silan-Ciruelas_BRA_Opt2_12B_MariaPaula_5-10_High_Median-High.pdf
DOI: 10.5061/dryad.gq567
title: Data from: Investigating the zoonotic origin of the West African Ebola epidemic

description: The severe Ebola virus disease epidemic occurring in West Africa stems
 from a single zoonotic transmission event to a 2-year-old boy in
 Meliandou, Guinea. We investigated the zoonotic origins of the epidemic
 using wildlife surveys, interviews, and molecular analyses of bat and
 environmental samples. We found no evidence for a concurrent outbreak in
 larger wildlife. Exposure to fruit bats is common in the region, but the
 index case may have been infected by playing in a hollow tree housing a
 colony of insectivorous free-tailed bats (Mops condylurus). Bats in this
 family have previously been discussed as potential sources for Ebola virus
 outbreaks, and experimental data have shown that this species can survive
 experimental infection. These analyses expand the range of possible Ebola
 virus sources to include insectivorous bats and reiterate the importance
 of broader sampling efforts for understanding Ebola virus ecology.
description: Partial mitochondrial
 cytochrome b and 16S sequences from bats captured in southeastern Guinea,
 2014Comprises all Sanger
 sequences generated for this study. Individuals were only assigned to the
 genus-level in the field. BLAST results were combined with this field
 assignment and further biological information (species distribution) to
 perform the final assignment. Sequence names are built as follows: sample
 #_final assignment.MariSaez_Bat_mtDNA.fastaPartial mitochondrial 16S sequences from soil samples from Meliandou, Guinea, 2014This ZIP file comprises demultiplexed FASTQ files corresponding to 30 PCR products sequenced on a MiSeq. A tab-delimited list is provided as the ReadMe.MariSaez_soil_16S_MiSeq.7z
DOI: 10.5064/f6vanjl8/qez0zg
title: Silan-Ciruelas_USA_Opt2_4B_Silky_1_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/afsrl5
title: Silan-Ciruelas_Opt2_Therapist6.pdf
DOI: 10.5061/dryad.r606d128
title: Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics

description: The field of phylogenetics is on the cusp of a major revolution, enabled
 by new methods of data collection that leverage both genomic resources and
 recent advances in DNA sequencing. Previous phylogenetic work has required
 labor-intensive marker development coupled with single-locus PCR and DNA
 sequencing on a clade-by-clade and marker-by-marker basis. Here, we
 present a new, cost-efficient, and rapid approach to obtaining data from
 hundreds of genes for potentially hundreds of individuals for deep and
 shallow phylogenetic studies. Specifically, we designed probes for target
 enrichment of &gt;500 loci in highly-conserved anchor regions of
 vertebrate genomes (flanked by less conserved regions) from five model
 species and tested enrichment efficiency in non-model species up to 254
 million years divergent from the nearest model. We found that hybrid
 enrichment using conserved probes (anchored enrichment) can recover a
 large number of unlinked loci that are useful at a diversity of
 phylogenetic timescales. This new approach has the potential to not only
 expedite resolution of deep-scale portions of the Tree of Life but also to
 greatly accelerate resolution of the large number of shallow clades that
 remain unresolved. The combination of low cost (~1% of the cost of
 traditional Sanger sequencing and ~3.5% of the cost of high-throughput
 amplicon sequencing for projects on the scale of 500 loci x 100
 individuals) and rapid data collection (~2 weeks of laboratory time) are
 expected to make this approach tractable even for researchers working on
 systems with limited or non-existent genomic resources.
description: Lemmon-etal2012_SupplementalMaterialsThis pdf document contains the Supplemental methods, results, figures and figures captions.Lemmon-etal2012_SupplementalTablesThis Excel file contains all of the supplemental tables and table captions.Lemmon-etal2012_AlignmentsLemmon-etal2012_ProbesLemmon-etal2012_ScriptsLemmon-etal2012_Phylogenetics_BUCKyLemmon-etal2012_Phylogenetics_BEST_Tetrapod_treeDistLemmon-etal2012_Phylogenetics_BEST_TetrapodLemmon-etal2012_Phylogenetics_BEST_Amniote_treeDistLemmon-etal2012_Phylogenetics_BEST_AmnioteLemmon-etal2012_Contigs
DOI: 10.5064/f6vanjl8/lzmutr
title: Silan-Ciruelas_FRA_Opt1_18B_20+_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/l7sc40
title: Silan-Ciruelas_USA_Opt2_23A_Silky_LGBTQ+AnyLength_Low_Median-High.pdf
DOI: 10.5061/dryad.63nd8
title: Data from: Using the generalized index of dissimilarity to detect gene-gene interactions in multi-class phenotypes

description: To find genetic association between complex diseases and phenotypic
 traits, one important procedure is conducting a joint analysis.
 Multifactor dimensionality reduction (MDR) is an efficient method of
 examining the interactions between genes in genetic association studies.
 It commonly assumes a dichotomous classification of the binary phenotypes.
 Its usual approach to determining the genomic association is to construct
 a confusion matrix to estimate a classification error, where a binary risk
 status is determined and assigned to each genotypic multifactor class.
 While multi-class phenotypes are commonly observed, the current MDR
 approach does not handle these phenotypes appropriately because the
 thresholds for the risk statuses may not be clear. In this study, we
 suggest a new method for estimating gene-gene interactions for multi-class
 phenotypes. Our approach adopts the index of dissimilarity (IDS) as an
 evaluation measure. This is analytically equivalent to the common
 association measure of balanced accuracy (BA) for the binary traits, while
 it is not required to determine the risk status for the estimation.
 Moreover, it is easily expandable to the generalized index of
 dissimilarity (GIDS), which has an explicit form that can handle any
 number of categories. The performance of the proposed method was compared
 with those of other approaches via simulation studies in which fifteen
 genetic models were generated with three class outcomes. A consistently
 better performance was observed using the proposed method. The effect of a
 varying number of categories was examined. The proposed method was also
 illustrated using real genome-wide association studies (GWAS) data from
 the Korean Association Resource (KARE) project.
description: Simulation Study I Data
 FileCompilation of the
 simulation data files, generated and analyzed for Simulation Study
 I.SimulationStudy-I.zipSimulation Study II Data FilesCompilation of simulation data files, generated and analyzed for Simulation Study II.SimulationStudy-II.zipGIDS calculation sampleGIDS calculation program along with a sample batch file, a sample data file, and output files. See Description.txt for detailed description.GIDS.zip
DOI: 10.5064/f6vanjl8/flmrhm
title: Silan-Ciruelas_USA_Opt2_7A_Silky_1-5_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/mtookv
title: Silan-Ciruelas_TUR_Opt2_23B_Anil_LGBT_Unknown_Median-High.pdf
DOI: 10.5061/dryad.33f97
title: Data from: Altered fronto-temporal functional connectivity in individuals at ultra-high-risk of developing psychosis

description: Background: The superior temporal gyrus (STG) is one of the key regions
 implicated in psychosis, given that abnormalities in this region are
 associated with an increased risk of conversion from an at-risk mental
 state to psychosis. However, inconsistent results regarding the functional
 connectivity strength of the STG have been reported, and the regional
 heterogeneous characteristics of the STG should be considered. Methods: To
 investigate the distinctive functional connection of each subregion in the
 STG, we parcellated the STG of each hemisphere into three regions: the
 planum temporale, Heschl’s gyrus, and planum polare. Resting-state
 functional magnetic resonance imaging was obtained from 22 first-episode
 psychosis (FEP) patients, 41 individuals at ultra-high-risk for psychosis
 (UHR), and 47 demographically matched healthy controls. Results:
 Significant group differences (in seed-based connectivity) were
 demonstrated in the left planum temporale and from both the right and left
 Heschl’s gyrus seeds. From the left planum temporale seed, the FEP and UHR
 groups exhibited increased connectivity to the bilateral dorsolateral
 prefrontal cortex. In contrast, the FEP and UHR groups demonstrated
 decreased connectivity from the bilateral Heschl’s gyrus seeds to the
 dorsal anterior cingulate cortex. The enhanced connectivity between the
 left planum temporale and right dorsolateral prefrontal cortex was
 positively correlated with positive symptom severity in individuals at UHR
 (r = .34, p = .03). Conclusions: These findings corroborate the
 fronto-temporal connectivity disruption hypothesis in schizophrenia by
 providing evidence supporting the altered fronto-temporal intrinsic
 functional connection at earlier stages of psychosis. Our data indicate
 that subregion-specific aberrant fronto-temporal interactions exist in the
 STG at the early stage of psychosis, thus suggesting that these
 aberrancies are the neural underpinning of proneness to psychosis.
description: Connectivity maps,
 demographics, and clinical assessmentsThe zip file contains
 Fisher’s Z transformed connectivity map of each ROI, restricted
 demographics of the participants, and their clinical
 assessments.Altered Fronto-Temporal
 Functional Connectivity in Individuals at Ultra-High-Risk of Developing
 Psychosis.zip
DOI: 10.5064/f6vanjl8/mcn1ya
title: Silan-Ciruelas_TUR_Opt2_10A_Sinem_5-10_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/rpu1rv
title: Silan-Ciruelas_PHL_Opt2-7B-Christelle_1-5_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/xvebak
title: Silan-Ciruelas_PublicCodebook.xlsx
DOI: 10.5061/dryad.57271
title: Data from: Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses

description: Mitochondrial DNA has been heavily utilized in phylogeography studies for
 several decades. However, underlying patterns of demography and
 phylogeography may be misrepresented due to coalescence stochasticity,
 selection, variation in mutation rates, and cultural hitchhiking (linkage
 of genetic variation to culturally transmitted traits affecting fitness).
 Cultural hitchhiking has been suggested as an explanation for low genetic
 diversity in species with strong social structures, counteracting even
 high mobility, abundance and limited barriers to dispersal. One such
 species is the sperm whale, which shows very limited phylogeographic
 structure and low mtDNA diversity despite a worldwide distribution and
 large population. Here, we use analyses of 175 globally distributed
 mitogenomes and three nuclear genomes to evaluate hypotheses of a
 population bottleneck/expansion versus a selective sweep due to
 cultural-hitchhiking or selection on mtDNA as the mechanism contributing
 to low worldwide mitochondrial diversity in sperm whales. In contrast to
 mtDNA control region (CR) data, mitogenome haplotypes are largely
 ocean-specific, with only one of 80 shared between the Atlantic and
 Pacific. Demographic analyses of nuclear genomes suggest low mtDNA
 diversity is consistent with a global reduction in population size that
 ended approximately 125,000 years ago, correlated with the Eemian
 interglacial. Phylogeographic analysis suggests that extant sperm whales
 descend from maternal lineages endemic to the Pacific during the period of
 reduced abundance, and have subsequently colonized the Atlantic several
 times. Results highlight the apparent impact of past climate change, and
 suggest selection and hitchhiking are not the sole processes responsible
 for low mtDNA diversity in this highly social species.
description: 4Pmac_wZiphiidae_Kbrev_200715_concat_modSites_100M4Pmac_wZiphiidae_Kbrev_200715_concat_modsites_100M4Pmac_wZiphiidae_Kbrev_200715_concat_modsites_100MAll_Pmac_Unique_hap_seqs_strict_100MAll_Pmac_Unique_hap_seqs_strict_100MAll_Pmac_Unique_hap_seqs_strict_100Mskygrid_24Jan2017skygrid_24Jan2017.logpma_mito_19Jan2017_skylineskyline_combined_trees_21Jan2017skyline_combined_log_21Jan2017Atl_pma_mito_19Jan2017_skylinePac_pma_mito_19Jan2017_skylineAtl_Pmac_mito_27Feb2017Pac_pma_mito_20Jan2017Atlpma_mito_27Feb2017Pac_pma_mito_27Feb2017
DOI: 10.5064/f6vanjl8/bm6swq
title: Silan-Ciruelas_PHL_Opt2_14A_Rozel_10-20_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/reqotf
title: Silan-Ciruelas_BRA_Opt2_24A_Camilla_LGBT_High_Median-High.pdf
DOI: 10.5061/dryad.ks5dr
title: Data from: Conservation planning for offsetting the impacts of development: a case study of biodiversity and renewable energy in the Mojave Desert

description: Balancing society's competing needs of development and conservation
 requires careful consideration of tradeoffs. Renewable energy development
 and biodiversity conservation are often considered beneficial
 environmental goals. However, the direct footprint and disturbance of
 renewable energy can displace species' habitat and negatively impact
 populations and communities if sited without ecological consideration. To
 mitigate residual impacts, offsets have emerged as a potentially useful
 tool after trying to avoid, minimize, or restore affected sites. Yet where
 many species or many sites are involved, the problem of efficiently
 designing a set of offset sites becomes increasingly complex. Spatial
 conservation prioritization tools are designed to handle this problem, but
 have seen little application to offset siting and analysis. To address
 this need we designed an offset siting support tool for the Desert
 Renewable Energy Conservation Plan (DRECP) of California, and present a
 case study of hypothetical impacts from solar development in the Western
 Mojave subsection. We compare two offset scenarios designed to mitigate a
 hypothetical 15,331 ha derived from proposed utility-scale solar energy
 development (USSED) projects. The first prioritizes offsets based
 precisely on impacted features, while the second offsets impacts based on
 the potential to maximize biodiversity conservation gains in the region.
 The two methods only agree on 28% of their prioritized sites and differ in
 meeting species-specific offset goals. Differences between the two
 scenarios highlight the importance of clearly specifying choices and
 priorities for offset siting and mitigation in general. Similarly, the
 effects of background climate and land use change may lessen the
 durability or effectiveness of offsets if not considered. Our offset
 siting support tool was designed specifically for the DRECP area, but with
 minor code modification could work well in other offset analyses, and
 provide continuing support for a potentially innovative mitigation
 solution to environmental impacts.
description: Data from Mojave Desert
 case studyThis data is from a case
 study of hypothetical impacts from solar development in the Western Mojave
 subsection. We compare two offset scenarios employing our offset siting
 support tool.Mojavset.7z
DOI: 10.5064/f6vanjl8/sakl1p
title: Silan-Ciruelas_USA_Opt2_20A_Marina_20_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/navgzj
title: Silan-Ciruelas_BRA_Opt2_15B_10_20_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/216kmx
title: Silan-Ciruelas_FRA_Opt1_2A_1_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/3gudg7
title: Silan-Ciruelas_USA_Opt2_3A_Silky_1_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/whte5x
title: Silan-Ciruelas_FRA_Opt1_4A_Hector_1_5_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/hgm37u
title: Silan-Ciruelas_USA_Opt2_12B_Haley_5-10_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/5uyemy
title: Silan-Ciruelas_FRA_Opt1_2B_1_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/cbrr43
title: Silan-Ciruelas_PHL_Opt2_3A_Donn_1_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/mc1gch
title: Silan-Ciruelas_FRA_Opt1_11B_5-10_Low_Median-High.pdf
DOI: 10.5061/dryad.p90b87p
title: Data from: Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird

description: Anthropogenic alterations to landscape structure and composition can have
 significant impacts on biodiversity, potentially leading to species
 extinctions. Population-level impacts of landscape change are mediated by
 animal behaviors, in particular dispersal behavior. Little is known about
 the dispersal habits of rails (Rallidae) due to their cryptic behavior and
 tendency to occupy densely vegetated habitats. The effects of landscape
 structure on the movement behavior of waterbirds in general are poorly
 studied due to their reputation for having high dispersal abilities. We
 used a landscape genetic approach to test hypotheses of landscape effects
 on dispersal behavior of the Hawaiian gallinule (Gallinula galeata
 sandvicensis), an endangered subspecies endemic to the Hawaiian Islands.
 We created a suite of alternative resistance surfaces representing
 biologically plausible a-priori hypotheses of how gallinules might
 navigate the landscape matrix, and ranked these surfaces by their ability
 to explain observed patterns in genetic distance among 12 populations on
 the island of O`ahu. We modeled effective distance among wetland locations
 on all surfaces using both cumulative least-cost-path and
 resistance-distance approaches, and evaluated relative model performance
 using Mantel tests, a causal modeling approach, and the mixed-model
 maximum-likelihood population-effects framework. Across all genetic
 markers, simulation methods, and model comparison metrics, surfaces that
 treated linear water features like streams, ditches, and canals as
 corridors for gallinule movement outperformed all other models. This is
 the first landscape-genetics study on the movement behavior of any
 waterbird species to our knowledge. Our results indicate that lotic water
 features, including drainage infrastructure previously thought to be of
 minimal habitat value, contribute to habitat connectivity in this listed
 subspecies.
description: HAGAFst_NonsigExcluded_3-14-17Genetic distance information between all pairs of sampled subpopulations of Hawaiian gallinules on OahuResistance_Surfaces_HAGAResistance surface ASCII layers used to generate effective distances between populations of Hawaiian gallinules on Oahuf_wet_negbin.zipCircuitscape__Resistance_DistancesResistance distances between all sampled Hawaiian gallinule populations on Oahu. Calculated using Circuitscape.EffectiveDistancesLeast-cost-path effective distances between all sampled populations of Hawaiian gallinules on Oahu. Calculated using Gdistance package in R.
DOI: 10.5064/f6vanjl8/jwqe5x
title: Silan-Ciruelas_PHL_Opt2_5A_Christelle_1-5_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/wy96kg
title: Silan-Ciruelas_PHL_Opt2_1B_Nica__1_Low_Low-Median.pdf
DOI: 10.5061/dryad.nf01p
title: Data from: Tectonic collision and uplift of Wallacea triggered the global songbird radiation

description: Songbirds (oscine passerines) are the most species rich and cosmopolitan
 bird group, comprising almost half of global avian species diversity.
 Because of their diversity and ubiquity, songbirds are used extensively in
 studies of evolutionary ecology, diversification, and ethology. Songbirds
 originated in Australia, but the evolutionary trajectory from a single
 species in an isolated continent to worldwide proliferation is poorly
 understood. Prior research suggested songbird diversification scenarios
 that are largely uncoupled from Earth history, including extensive
 diversification of lineages in New Guinea prior to its emergence as a
 landmass and long-distance dispersal to Africa or Asia when no dispersal
 corridors existed. However, these results may be flawed because the
 studies relied on unresolved phylogenetic relationships and a
 controversial biogeographic time calibration. Here, we combine the first
 genome-scale DNA sequence data set for songbirds, fossil-based time
 calibrations, and geologically informed biogeographic reconstructions to
 provide the first well-supported evolutionary hypothesis for the group. We
 show that songbird diversification began in the Oligocene, but accelerated
 in the early Miocene, at approximately half the age of most previous
 estimates. This burst of diversification occurred after island formation
 in Wallacea, which provided the first dispersal corridor out of Australia,
 and resulted in independent waves of songbird expansion through Asia to
 the rest of the globe. Although New Guinea presently contains high
 songbird species richness, our data unambiguously falsify the proto-Papuan
 hypothesis for early songbird diversification and suggest that New Guinea
 has, instead, served as an “evolutionary refuge” for Australian lineages
 that have diversified more recently within the island. Our results
 reconcile songbird evolution with Earth history and link a major radiation
 of terrestrial biodiversity to early diversification within an isolated
 Australian continent.
description: 1.Moyle.oscine.UCE.completematrixComplete (loci common to all taxa) matrix of oscine UCE data. Date were produced with the tetrapod UCE 5K probe kit from Mycroarray. Data aligned with MAFFT, and trimmed with Gblocks. Number after taxon name refers to sample number.2.Moyle.oscine.UCE.incompletematrixIncomplete 75% matrix (loci common to at least 75% of taxa) of oscine UCE data. Date were produced with the tetrapod UCE 5K probe kit from Mycroarray. Data aligned with MAFFT, and trimmed with Gblocks. Number after taxon name refers to sample number. Character set information at end of file partitions data according to evolutionary model.
DOI: 10.5064/f6vanjl8/kqkc7k
title: Silan-Ciruelas_DataNarrative.pdf
DOI: 10.5064/f6vanjl8/gyrzkp
title: Silan-Ciruelas_USA_Opt2_6A_Jon_1-5_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/7xv1bv
title: Silan-Ciruelas_Opt2_Therapist7.pdf
DOI: 10.5064/f6vanjl8/sq7v8k
title: Silan-Ciruelas_FRA_Opt1_20B_20+_High_Median-High.pdf