cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r7pc5
title: Data from: Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic

description: Changing climate is expected to alter precipitation patterns in the
 Arctic, with consequences for subsurface temperature and moisture
 conditions, community structure, and nutrient mobilization through
 microbial belowground processes. Here, we address the effect of increased
 snow depth on the variation in species richness and community structure of
 ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected
 weekly from mid-July to mid-September in both control and deep snow plots.
 Richness of ECM fungi was lower, while saprotrophic fungi was higher in
 increased snow depth plots relative to controls. [Correction added on 23
 September 2016 after first online publication: In the preceding sentence,
 the richness of ECM and saprotrophic fungi were wrongly interchanged and
 have been fixed in this current version.] ECM fungal richness was related
 to soil NO3-N, NH4-N, and K; and saprotrophic fungi to NO3-N and pH. Small
 but significant changes in the composition of saprotrophic fungi could be
 attributed to snow treatment and sampling time, but not so for the ECM
 fungi. Delayed snow melt did not influence the temporal variation in
 fungal communities between the treatments. Results suggest that some
 fungal species are favored, while others are disfavored resulting in their
 local extinction due to long-term changes in snow amount. Shifts in
 species composition of fungal functional groups are likely to affect
 nutrient cycling, ecosystem respiration, and stored permafrost carbon.
description: F_L001_R1.fastqPaired-end Illumina seqeuncing output fastq file with forward readsF_L001_R2.fastqPaired-end Illumina seqeuncing output fastq file with reverse readsmapfile_fsoilMapping file associated with sequencing read files.
DOI: 10.5061/dryad.288c2
title: Data from: Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections

description: Model selection approaches in phylogeography have allowed researchers to
 evaluate the support for competing demographic histories, which provides a
 mode of inference and a measure of uncertainty in understanding climatic
 and spatial influences on intraspecific diversity. Here, to rank all
 models in the comparison set, and determine what proportion of the total
 support the top-ranked model garners, we conduct model selection using two
 analytical approaches –allele frequency-based, implemented in
 fastsimcoal2, and gene tree-based, implemented in PHRAPL. We then expand
 this model-selection framework by including an assessment of absolute fit
 of the models to the data. For this, we utilize DNA isolated from existing
 natural history collections that span the distribution of red alder (Alnus
 rubra) in the Pacific Northwest of North America to generate genomic data
 for the evaluation of 13 demographic scenarios. The quality of DNA
 recovered from herbarium specimen leaf tissue was assessed for its utility
 and effectiveness in demographic model selection, specifically in the two
 approaches mentioned. We present strong support for the use of herbarium
 tissue in the generation of genomic DNA, albeit with the inclusion of
 additional quality control checks prior to library preparation and
 analyses with multiple approaches that incorporate various data. Analyses
 with allele frequency spectra and gene trees predominantly support A.
 rubra having experienced an ancient vicariance event with intermittent and
 frequent gene flow between the disjunct populations. Additionally, the
 data consistently fit the most frequently selected model, corroborating
 the model selection techniques. Finally, these results suggest that the A.
 rubra disjunct populations do not represent separate species.
description: GeneTree_DataFiles.tarjAFS_dataFiles.taralnusBarcodesBarcodes to process ddRAD dataAlnus_R1Alnus rubra paired-end ddRadseq; R1 reads. fastq.gz file ~2.95GBAlnus_R2Alnus rubra paired-end ddRadseq; R2 reads. fastq.gz file ~2.95GB
DOI: 10.5061/dryad.cs604
title: Data from: Evidence accumulation and choice maintenance are dissociated in human perceptual decision making

description: Perceptual decision making in monkeys relies on decision neurons, which
 accumulate evidence and maintain choices until a response is given. In
 humans, several brain regions have been proposed to accumulate evidence,
 but it is unknown if these regions also maintain choices. To test if
 accumulator regions in humans also maintain decisions we compared delayed
 and self-paced responses during a face/house discrimination decision
 making task. Computational modeling and fMRI results revealed dissociated
 processes of evidence accumulation and decision maintenance, with
 potential accumulator activations found in the dorsomedial prefrontal
 cortex, right inferior frontal gyrus and bilateral insula. Potential
 maintenance activation spanned the frontal pole, temporal gyri, precuneus
 and the lateral occipital and frontal orbital cortices. Results of a
 quantitative reverse inference meta-analysis performed to differentiate
 the functions associated with the identified regions did not narrow down
 potential accumulation regions, but suggested that response-maintenance
 might rely on a verbalization of the response.
description: S20fMRI and behavioral data
 for subject 2020.tarS22fMRI and behavioral data for subject 2222.tarS23fMRI and behavioral data for subject 2323.tarS24fMRI and behavioral data for subject 2424.tarS25fMRI and behavioral data for subject 2525.tarS26fMRI and behavioral data for subject 2626.tarS27fMRI and behavioral data for subject 2727.tarS28fMRI and behavioral data for subject 2828.tarS29fMRI and behavioral data for subject 2929.tarS30fMRI and behavioral data for subject 3030.tarS31fMRI and behavioral data for subject 3131.tarS32fMRI and behavioral data for subject 3232.tarS34fMRI and behavioral data for subject 3434.tarS35fMRI and behavioral data for subject 3535.tarS36fMRI and behavioral data for subject 3636.tarS37fMRI and behavioral data for subject 3737.tarS38fMRI and behavioral data for subject 3838.tarS39fMRI and behavioral data for subject 3939.tar
DOI: 10.5061/dryad.3075h
title: Data from: Early and dynamic colonization of Central America drives speciation in Neotropical army ants

description: The emergence of the Isthmus of Panama is one of the most important events
 in recent geological history, yet its timing and role in fundamental
 evolutionary processes remain controversial. While the formation of the
 isthmus was complete around 3 million years ago (Ma), recent studies have
 suggested prior intercontinental biotic exchange. In particular, the
 possibility of early intermittent land bridges facilitating colonization
 constitutes a potential mechanism for speciation and colonization before
 full closure of the isthmus. To test this hypothesis, we employed genomic
 methods to study the biogeography of the army ant genus Eciton, a group of
 keystone arthropod predators in Neotropical rainforests. Army ant colonies
 are unable to disperse across water and are therefore ideally suited to
 study the biogeographic impact of land bridge formation. Using a reduced
 representation genome sequencing approach, we show that all strictly
 Central American lineages of Eciton diverged from their respective South
 American sister lineage between 4 and 7 Ma, significantly prior to the
 complete closure of the isthmus. Furthermore, three of the lineage pairs
 form extensive and coincident secondary contact zones in Costa Rica and
 Nicaragua, with no evidence of gene flow. Such a discrete and repeated
 biogeographic pattern indicates at least two waves of army ant dispersal
 into Central America that were separated by significant genetic divergence
 times. Thus, by integrating phylogenomic, population genomic and
 geographic evidence, we show that early colonization of Central America
 across the emerging Isthmus of Panamá drove parallel speciation in Eciton
 army ants.
description: Concatenated data
 matrixconcatenated_data_matrix.phy
DOI: 10.5061/dryad.2r746
title: Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic

description: California vernal pool (VP) ecosystems support a diverse community of
 endemic plants that are threatened by multiple anthropogenic pressures,
 generating a need for molecular tools to quantify the extent and
 distribution of genetic variation in native populations. Here, we used
 RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread
 VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based
 SNPs using a RAD-tag library of 12 individuals from different VP complexes
 using SbfI, a restriction enzyme that does not cleave the chloroplast
 genome in Lasthenia. A total of 316,106 catalog loci were obtained across
 all twelve individuals in the library. Of these, 713 loci were
 polymorphic, yielding 3918 candidate SNPs. Next, we genotyped an
 additional 285 additional plants to validate and characterize 71 of the
 candidate SNPs. Of these, 44 were polymorphic among VP complexes. A
 preliminary analysis of the distribution of genetic variation using these
 loci revealed significant isolation-by-distance across the species’
 geographic range. Weaker, but in some cases significant, genetic
 differentiation was detected among subpopulations from different pools
 within a single VP complex. Thus, in this study, RADseq allowed the
 discovery of SNP markers that can characterize patterns of genetic
 variation at multiple spatial scales in L. fremontii, which can be used to
 inform the conservation and mitigation of VP populations.
description: FremontiiRAD2013_rawreads_replacedFremontiiRAD2013_rawreads.fastq.zip
DOI: 10.5061/dryad.vv527
title: Data from: Controlling for p-value inflation in allele frequency change in experimental evolution and artificial selection experiments

description: Experimental evolution studies can be used to explore genomic response to
 artificial and natural selection. In such studies, loci that display
 larger allele frequency change than expected by genetic drift alone are
 assumed to be directly or indirectly associated with traits under
 selection. However, such studies report surprisingly many loci under
 selection, suggesting that current tests for allele frequency change may
 be subject to p-value inflation and hence be anti-conservative. One factor
 known from genome wide association (GWA) studies to cause p-value
 inflation is population stratification, such as relatedness among
 individuals. Here we suggest that by treating presence of an individual in
 a population after selection as a binary response variable, existing GWA
 methods can be used to account for relatedness when estimating allele
 frequency change. We show that accounting for relatedness like this
 effectively reduces false positives in tests for allele frequency change
 in simulated data with varying levels of population structure. However,
 once relatedness has been accounted for, the power to detect causal loci
 under selection is low. Finally, we demonstrate the presence of p-value
 inflation in allele frequency change in empirical data spanning multiple
 generations from an artificial selection experiment on tarsus length in
 two wild populations of house sparrow, and correct for this using genomic
 control. Our results indicate that since allele frequencies in large parts
 of the genome may change when selection acts on a heritable trait, such
 selection is likely to have considerable and immediate consequences for
 the eco-evolutionary dynamics of the affected populations.
description: DataThis file contains a
 folder with all raw data for the simulations. More instructions can be
 found in file "Simulated_data.R" available from the data file
 "Rproject".RProjectThis file contains folder with the complete RProject for this manuscript, minus the original data files for the simulation project (available as file "Data.tar.gz"). All other temporary (.rda) data files are in in this folder as well.Rproject.tar.gz
DOI: 10.5061/dryad.2n6p6
title: Data from: Stability of the gorilla microbiome despite simian immunodeficiency virus infection

description: Simian immunodeficiency viruses (SIVs) have been discovered in over 45
 primate species; however, the pathogenic potential of most SIV strains
 remains unknown due to difficulties inherent in observing wild
 populations. Because those SIV infections that are pathogenic have been
 shown to induce changes in the host's gut microbiome, monitoring the
 microbiota present in faecal samples can provide a noninvasive means for
 studying the effects of SIV infection on the health of wild-living
 primates. Here, we examine the effects of SIVgor, a close relative of
 SIVcpz of chimpanzees and HIV-1 of humans, on the gut bacterial
 communities residing within wild gorillas, revealing that gorilla gut
 microbiomes are exceptionally robust to SIV infection. In contrast to the
 microbiomes of HIV-1-infected humans and SIVcpz-infected chimpanzees,
 SIVgor-infected gorilla microbiomes exhibit neither rises in the
 frequencies of opportunistic pathogens nor elevated rates of microbial
 turnover within individual hosts. Regardless of SIV infection status,
 gorilla microbiomes assort into enterotypes, one of which is
 compositionally analogous to those identified in humans and chimpanzees.
 The other gorilla enterotype appears specialized for a leaf-based diet and
 is enriched in environmentally derived bacterial genera. We hypothesize
 that the acquisition of this gorilla-specific enterotype was enabled by
 lowered immune system control over the composition of the microbiome. Our
 results indicate differences between the pathology of SIVgor and
 SIVcpz/HIV-1 infections, demonstrating the utility of investigating host
 microbial ecology as a means for studying disease in wild primates of high
 conservation priority.
description: gorilladataGorBonUTaustin.fastq
DOI: 10.5061/dryad.bt703
title: Data from: Comparing analysis methods in functional calcium imaging of the insect brain

description: We investigate four different methods for background estimation in calcium
 imaging of the insect brain and evaluate their performance on six data
 sets consisting of data recorded from two sites in two species of moths.
 The calcium fluorescence decay curve outside the potential response is
 estimated using either a low-pass filter or constant, linear or polynomial
 regression, and is subsequently used to calculate the magnitude, latency
 and duration of the response. The magnitude and variance of the responses
 that are obtained by the different methods are compared, and, by computing
 the receiver operating characteristics of a classifier based on response
 magnitude, we evaluate the ability of each method to detect the stimulus
 type and conclude that a polynomial approximation of the background gives
 the overall best result.
description: Optical Imaging Data
 SetsSix data sets with
 optical imaging sequences from Manduca sexta and Cydia
 pomonella.DataSets.zip
DOI: 10.5061/dryad.n3v49
title: Data from: Phylosymbiosis: relationships and functional effects of microbial communities across host evolutionary history

description: Phylosymbiosis was recently proposed to describe the eco-evolutionary
 pattern whereby the ecological relatedness of host-associated microbial
 communities parallels the phylogeny of related host species. Here, we
 analyze the prevalence of phylosymbiosis and its functional significance
 under highly controlled conditions by characterizing the microbiota of 24
 animal species from four different groups (Peromyscus deer mice,
 Drosophila flies, mosquitoes, Nasonia wasps) and re-evaluate the
 phylosymbiotic relationships of seven species of wild hominids. We
 demonstrate three key findings. First, intraspecific microbiota variation
 is consistently less than interspecific microbiota variation, and
 microbiota-based models predict host species origin with high accuracy
 across the dataset. Interestingly, the age of host clade divergence
 positively associates with the degree of intraspecific microbial community
 distinguishability within the host clades, spanning recent host speciation
 (~one million years ago) to more distantly related host genera (~108
 million years ago). Second, various topological congruence analyses of
 each group's phylogeny and microbiota dendrogram reveal significant
 degrees of phylosymbiosis, irrespective of host clade age or taxonomy.
 Third, experimental transplants of autochthonous (intraspecific) versus
 allochthonous (interspecific) microbiota among closely related wasp
 species and more divergent mice species demonstrate reductions in host
 survival and digestive performance, respectively. Consistent with
 selection on host-microbiota interactions driving phylosymbiosis, there
 are survival and performance reductions when interspecific microbiota
 transplants are conducted between closely-related and divergent host
 species pairs. Overall these findings indicate that the composition and
 functional effects of an animal's microbial community can be closely
 allied with host evolution, even across wide-ranging timescales and in
 diverse animal systems reared under controlled conditions.
description: Raw
 sequencesraw_sequences.zip
DOI: 10.5061/dryad.9nv3b
title: Data from: Temporal regularity increases with repertoire complexity in the Australian pied butcherbird’s song

description: Music maintains a characteristic balance between repetition and novelty.
 Here, we report a similar balance in singing performances of free-living
 Australian pied butcherbirds. Their songs include many phrase types. The
 more phrase types in a bird's repertoire, the more diverse the
 singing performance can be. However, without sufficient temporal
 organization, avian listeners may find diverse singing performances
 difficult to perceive and memorize. We tested for a correlation between
 the complexity of song repertoire and the temporal regularity of singing
 performance. We found that different phrase types often share motifs
 (notes or stereotyped groups of notes). These shared motifs reappeared in
 strikingly regular temporal intervals across different phrase types, over
 hundreds of phrases produced without interruption by each bird. We
 developed a statistical estimate to quantify the degree to which phrase
 transition structure is optimized for maximizing the regularity of shared
 motifs. We found that transition probabilities between phrase types tend
 to maximize regularity in the repetition of shared motifs, but only in
 birds of high repertoire complexity. Conversely, in birds of low
 repertoire complexity, shared motifs were produced with less regularity.
 The strong correlation between repertoire complexity and motif regularity
 suggests that birds possess a mechanism that regulates the temporal
 placement of shared motifs in a manner that takes repertoire complexity
 into account. We discuss alternative musical, mechanistic and ecological
 explanations to this effect.
description: Audio_Bird1Audio_Bird2Audio_Bird3Audio_Bird4Audio_Bird5Audio_Bird6Audio_Bird7Audio_Bird8Audio_Bird9Audio_Bird10Audio_Bird11Audio_Bird12Audio_Bird13Audio_Bird14Audio_Bird15Audio_Bird16Audio_Bird17
DOI: 10.5061/dryad.km22nh0
title: Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses

description: Switchgrass is a promising herbaceous energy crop, but further gains in
 biomass yield and quality must be achieved to enable a viable bioenergy
 industry. Developing DNA markers can contribute to such progress, but
 depiction of genetic bases should be reliable, involving not only simple
 additive marker effects but also interactions with genetic backgrounds,
 e.g., ecotypes, or synergies with other markers. We analyzed plant height,
 carbon content, nitrogen content, and mineral concentration in a diverse
 panel consisting of 512 genotypes of upland and lowland ecotype. We
 performed association analyses based on exome capture sequencing and
 tested 439,170 markers for marginal effects, but also 83,290 markers for
 marker-by-ecotype interactions and up to 311,445 marker pairs for pairwise
 interactions. Analyses of pairwise interactions focused on subsets of
 marker pairs preselected based on marginal marker effects, gene ontology
 annotation, and pairwise marker associations. Our tests identified 12
 significant effects. Homology and gene expression information corroborated
 seven effects and indicated plausible causal pathways: flowering time and
 lignin synthesis for plant height; plant growth and senescence for carbon
 content and mineral concentration. Four pairwise interactions were
 detected, including three interactions preselected based on pairwise
 marker correlations. Furthermore, one marker-by-ecotype interaction and
 one pairwise interaction were confirmed in an independent switchgrass
 panel. Our analyses identified reliable candidate variants for important
 bioenergy traits in switchgrass. Moreover, they exemplified the importance
 of interactive effects for the depiction of genetic bases, and illustrated
 the usefulness of preselection of marker pairs for identifying pairwise
 marker interactions in association testing.
description: raw_SNP.txt.gzcompressed gz file containing read counts at unfiltered SNPs in NAP and SAPformatted_SNP.zipcompressed zip file containing genotype calls at filtered SNPs in NAP and SAP (formatted_SNP.csv), NAP only (formatted_SNP-NAP.csv) or SAP only (formatted_SNP-SAP.csv)raw_phenotype.zipcompressed zip file containing raw phenotypic data in NAP (raw_phenotype-NAP.csv) or SAP (raw_phenotype-SAP.csv)genotype_means.zipcompressed zip file containing estimated genotype means in NAP (genotype_means-NAP.csv) or SAP (genotype_means-SAP.csv)READMEREADME