cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.15570
title: Data from: Divergence in coloration and the evolution of reproductive isolation in the Anolis marmoratus species complex

description: Adaptive divergence in coloration is expected to produce reproductive
 isolation in species that use colorful signals in mate choice and species
 recognition. Indeed, many adaptive radiations are characterized by
 differentiation in colorful signals, suggesting that divergent selection
 acting on coloration may be an important component of speciation.
 Populations in the Anolis marmoratus species complex from the Caribbean
 island of Guadeloupe display striking divergence in adult male color and
 pattern that occurs over small geographic distances, suggesting strong
 divergent selection. Here we test the hypothesis that coloration is
 locally adaptive and is linked to reduced gene flow among populations. We
 quantify variation in adult male coloration across a habitat gradient
 between mesic and xeric habitats, use a multilocus coalescent approach to
 infer historical demographic parameters of divergence, and examine gene
 flow and population structure using microsatellite variation. We find that
 color variation evolved without geographic isolation and in the face of
 rampant gene flow, consistent with strong divergent selection, and that
 both ecological and sexual selection are implicated. However, we find no
 significant differentiation at microsatellite loci across populations,
 suggesting little reproductive isolation and high levels of contemporary
 gene exchange. Strong divergent selection on loci affecting coloration
 likely maintains clinal phenotypic variation despite high gene flow at
 neutral loci, supporting the notion of a porous genome in which adaptive
 portions of the genome remain fixed while neutral portions are homogenized
 by gene flow and recombination. We discuss the impact of these findings
 for studies of color evolution and ecological speciation.
description: MarthaIMaInputInput file used to conduct IMa analysis for historical demographic analysis of Anolis marmoratus on the island of Grande Terre.Spectral_FoldersThe files in each folder are the raw spectral reflectance values for male lizards, female lizards, and vegetation. A key is provided for the male and female lizard files. Files that have duplicate sample numbers represent repeated measures.Munoz_etal_2013_msat_datasetMicrosatellite data used for demographic analyses. Loci and scores are given for each individual from each population.
DOI: 10.25345/c50g3hb9h
title: MassIVE MSV000100600 - Stimulation of UDP-Glucose or SDF-1 to Optimize Responsiveness of Hematopoietic Stem/Progenitor Cells to profile metabolic changes
title: Purinergic signaling plays a crucial role in hematopoietic stem/progenitor cell (HSPC) trafficking, and the role of the extracellular purinergic alarmin adenosine triphosphate (ATP) is well established. Another alarmin, uridine diphosphate glucose (UDP-glucose), has also been reported to promote HSPC mobilization after binding to the P2Y14 purinergic receptor. To address this data at the molecular level, we performed metabolomics studies and, after analyzing SDF-1, UDP-G, or SDF-1+UDP-G-induced stimulations, we identified several significant changes in lipid raft formation-related metabolites.
DOI: 10.5061/dryad.g860v
title: Data from: Comparing G: multivariate analysis of genetic variation in multiple populations

description: The additive genetic variance–covariance matrix (G) summarizes the
 multivariate genetic relationships among a set of traits. The geometry of
 G describes the distribution of multivariate genetic variance, and
 generates genetic constraints that bias the direction of evolution.
 Determining if and how the multivariate genetic variance evolves has been
 limited by a number of analytical challenges in comparing G-matrices.
 Current methods for the comparison of G typically share several drawbacks:
 metrics that lack a direct relationship to evolutionary theory, the
 inability to be applied in conjunction with complex experimental designs,
 difficulties with determining statistical confidence in inferred
 differences and an inherently pair-wise focus. Here, we present a cohesive
 and general analytical framework for the comparative analysis of G that
 addresses these issues, and that incorporates and extends current methods
 with a strong geometrical basis. We describe the application of random
 skewers, common subspace analysis, the 4th-order genetic covariance tensor
 and the decomposition of the multivariate breeders equation, all within a
 Bayesian framework. We illustrate these methods using data from an
 artificial selection experiment on eight traits in Drosophila serrata,
 where a multi-generational pedigree was available to estimate G in each of
 six populations. One method, the tensor, elegantly captures all of the
 variation in genetic variance among populations, and allows the
 identification of the trait combinations that differ most in genetic
 variance. The tensor approach is likely to be the most generally
 applicable method to the comparison of G-matrices from any sampling or
 experimental design.
description: Aguirre_et_al_
 data_ped_outputThe zip file contains
 that data and pedigree files for the results presented in the manuscript.
 Also included are the example output files to be used in the attached
 .docx tutorial. Last a .r file is attached as an example of a script used
 to generate the output files.
DOI: 10.5061/dryad.2fs2b
title: Data from: A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets

description: It has been proposed that supertree approaches should be applied to large
 multilocus sequence datasets to achieve computational tractability. Large
 datasets such as those derived from phylogenomics studies can be broken
 into many locus-specific tree searches and the resulting trees can be
 stitched together via a supertree method. Using simulated data, workers
 have reported that they can rapidly construct a supertree that is
 comparable to the results of heuristic tree search on the entire dataset.
 To test this assertion with organismal data, we compared tree length under
 the parsimony criterion and computational time for twenty multilocus
 datasets using supertree (SuperFine and SuperTriplets) and supermatrix
 (heuristic search in TNT) approaches. Tree length and computational times
 were compared among methods using the Wilcoxon matched-pairs signed rank
 test. Supermatrix searches produce significantly shorter trees than either
 supertree approach (SuperFine or SuperTriplets; p &lt; 0.0002 in both
 cases). Moreover, the processing time of supermatrix search was
 significantly lower than SuperFine+locus-specific search (p &lt; 0.01)
 but roughly equivalent to that of SuperTriplets+locus-specific search (p
 &gt; 0.4, not significant). In conclusion, we show by using real
 rather than simulated data, that there is no basis, either in time
 tractability or tree length, for use of supertrees over heuristic tree
 search using a supermatrix for phylogenomics.
description: RawDataTwenty multilocus sequence datasets used in supertree versus supermatrix comparisons
DOI: 10.5061/dryad.25696
title: Data from: Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

description: Massively parallel sequencing has enabled the creation of novel, in-depth
 genetic tools for nonmodel, ecologically important organisms. We present
 the de novo transcriptome sequencing, analysis and microarray development
 for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of
 ecological and evolutionary interest, especially with respect to ingestion
 and hepatic metabolism of potentially toxic plant secondary compounds. We
 generated a liver transcriptome of the desert woodrat (Neotoma lepida)
 using the Roche 454 platform. The assembled contigs were well annotated
 using rodent references (99.7% annotation), and biotransformation function
 was reflected in the gene ontology. The transcriptome was used to develop
 a custom microarray (eArray, Agilent). We tested the microarray with three
 experiments: one across species with similar habitat (thus, dietary)
 niches, one across species with different habitat niches and one across
 populations within a species. The resulting one-colour arrays had high
 technical and biological quality. Probes designed from the woodrat
 transcriptome performed significantly better than functionally similar
 probes from the Norway rat (Rattus norvegicus). There were a multitude of
 expression differences across the woodrat treatments, many of which
 related to biotransformation processes and activities. The pattern and
 function of the differences indicate shared ecological pressures, and not
 merely phylogenetic distance, play an important role in shaping gene
 expression profiles of woodrat species and populations. The quality and
 functionality of the woodrat transcriptome and custom microarray suggest
 these tools will be valuable for expanding the scope of herbivore biology,
 as well as the exploration of conceptual topics in ecology.
description: qPCRvalid_Neo_arrayTable2_rattusVneo_allprobesTable2_matchedprobes_bothCompTable2_LRvsPS_Neoprobes
DOI: 10.5061/dryad.tm093
title: Data from: Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander

description: Tropical montane taxa are often locally adapted to very specific climatic
 conditions, contributing to their lower dispersal potential across complex
 landscapes. Climate and landscape features in montane regions affect
 population genetic structure in predictable ways, yet few empirical
 studies quantify the effects of both factors in shaping genetic structure
 of montane-adapted taxa. Here, we considered temporal and spatial
 variability in climate to explain contemporary genetic differentiation
 between populations of the montane salamander, Pseudoeurycea leprosa.
 Specifically, we used ecological niche modelling (ENM) and measured
 spatial connectivity and gene flow (using both mtDNA and microsatellite
 markers) across extant populations of P. leprosa in the Trans-Mexican
 Volcanic Belt (TVB). Our results indicate significant spatial and genetic
 isolation among populations, but we cannot distinguish between isolation
 by distance over time or current landscape barriers as mechanisms shaping
 population genetic divergences. Combining ecological niche modelling,
 spatial connectivity analyses, and historical and contemporary genetic
 signatures from different classes of genetic markers allows for inference
 of historical evolutionary processes and predictions of the impacts future
 climate change will have on the genetic diversity of montane taxa with low
 dispersal rates. Pseudoeurycea leprosa is one montane species among many
 endemic to this region and thus is a case study for the continued
 persistence of spatially and genetically isolated populations in the
 highly biodiverse TVB of central Mexico.
description: All_ENMpointsThis file contains latitude and longitude coordinates for localities used to construct species distribution models.Structure infileInput file for Structure analysis.P. leprosa_genotypes.txtCCSA_conductance_infileConductance grid obtained from ENMs (LGM, CCSA3) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.CCSA_conductance.ascMIROC_conductance_infileConductance grid obtained from ENMs (LGM, MIROC) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.MIROC_conductance.asc2050_conductance_infileConductance grid obtained from ENMs (Future, 2050) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.2050_conductance.ascPresent_conductance_infileConductance grid obtained from ENMs (Present time) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.Present_conductance.ascLandcover_conductance_infileConductance grid obtained from ENMs (Land cover) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.Landcover_conductance.ascTopography_conductance_infileConductance grid obtained from ENMs (Topography) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.Topography_conductance.asc
DOI: 10.5061/dryad.t1n04
title: Data from: Macaque monkeys perceive the flash lag illusion

description: Transmission of neural signals in the brain takes time due to the slow
 biological mechanisms that mediate it. During such delays, the position of
 moving objects can change substantially. The brain could use statistical
 regularities in the natural world to compensate neural delays and
 represent moving stimuli closer to real time. This possibility has been
 explored in the context of the flash lag illusion, where a briefly flashed
 stimulus in alignment with a moving one appears to lag behind the moving
 stimulus. Despite numerous psychophysical studies, the neural mechanisms
 underlying the flash lag illusion remain poorly understood, partly because
 it has never been studied electrophysiologically in behaving animals.
 Macaques are a prime model for such studies, but it is unknown if they
 perceive the illusion. By training monkeys to report their percepts
 unbiased by reward, we show that they indeed perceive the illusion
 qualitatively similar to humans. Importantly, the magnitude of the
 illusion is smaller in monkeys than in humans, but it increases linearly
 with the speed of the moving stimulus in both species. These results
 provide further evidence for the similarity of sensory information
 processing in macaques and humans and pave the way for detailed
 neurophysiological investigations of the flash lag illusion in behaving
 macaques.
description: raw_data_monkeyraw_data_humanRaw behavioral data collected from eight human subjects.pooled_data_monkeysBehavioral response data of monkeys, pooled across sessions. This is computed from raw_data_monkey.mat file.pooled_data_humansBehavioral response data from humans, pooled across sessions. This is computed from raw_data_human.mat file.fit_data_pooled_monkeysPsychometric function fit data for monkeys' behavioral responses.fit_data_pooled_humansPsychometric function fit data of behavioral responses of human subjects.xyn_fig_2ABehavioral response data from monkey B used for psychometric function fit shown in Figure 2A in the paper.fit_data_fig_2APsychometric function fit data for responses in xyn_fig_2A.mat file.data_monkeys_by_testing_dayPsychometric function fit data for behavioral sessions of monkeys.data_humans_by_testing_dayPsychometric function fit data for each testing day of human subjects.data_humans_single_sessPsychometric function fit data for each sitting of behavioral testing in humans.stat_data_for_fig_2_3_4Spatial lag and slope data used for statistics associated with Figures 2,3 and 4stat_data_for_fig_5ABSpatial lag and slope data need for statistics associated with Figure 5A and 5B.stat_data_for_fig_5CSpatial lag and slope data for statistics associated with Figure 5C.stat_data_for_fig_2_3_4Spatial lag and slope data for statistics associated with Figures 2, 3 and 4.stat_data_for_fig_5ABSpatial lag and slope data for statistics associated with Figure 5A and 5B.stat_data_for_fig_5CSpatial lag and slope data for statistics associated with Figure 5C.readmepdf version of readme.txt. This file contains all the details needed to reproduce Figures and results of the paper.
DOI: 10.5061/dryad.qb753
title: Data from: Identification and evaluation of novel acetolactate synthase inhibitors as antifungal agents

description: High-throughput phenotypic screening against yeast Saccharomyces
 cerevisiae revealed a series of triazolo-pyrimidine-sulfonamide compounds
 with broad-spectrum antifungal activity, no significant cytotoxicity, and
 low protein binding. To elucidate the target of this series we have
 applied a chemogenomic profiling approach using the S. cerevisiae deletion
 collection. All compounds of the series yielded highly similar profiles
 that suggested acetolactate synthase (Ilv2p, catalyzes the first common
 step in branched chain amino acid biosynthesis) as a possible target. High
 correlation to profiles of known Ilv2p inhibitors like chlorimuron-ethyl
 provided further evidence for a similar mechanism of action. Genome-wide
 mutagenesis in S. cerevisiae identified 13 resistant clones with 3
 different mutations in the catalytic subunit of acetolactate synthase that
 also conferred cross-resistance to established Ilv2p inhibitors. Mapping
 the mutations into the published Ilv2p crystal structure outlined the
 chlorimuron-ethyl binding cavity and it was possible to dock the
 triazolo-pyrimidine-sulfonamide compound into this pocket in silico.
 However, fungal growth inhibition could be bypassed through
 supplementation with exogenous branched chain amino acids, or by the
 addition of serum to the medium in all of the fungal organisms tested
 except for Aspergillus fumigatus. Thus, these data support the
 identification of triazolo-pyrimidine-sulfonamide as inhibitors of
 acetolactate synthase but suggest that targeting may be compromised due to
 the possibility of nutrient bypass in vivo.
description: Supplemental_Data.zipThe compressed Supplemental_Data.zip archive contains two files: 1. Supplemental Data_S3, the complete HIP HOP profiles are provided as tab delimited .txt files. The sensitivity and z-scores for all HIP strains present in the pool across all tested compounds are listed in the HIP-exp-scores-annotation.txt file, scores for all HOP strains present in the pool are listed in the HOP-exp-scores-annotation.txt file. To reproduce the plots depicted in the article the sensitivity can be plotted on the y-axis, the z-score on the x-axis. Each gene is annotated with systematic name, common name, description, GO category etc. 2. The Supplemental_Data_S4.zip file containing the in silico docking solution. It is provided as a standard Protein Data Bank file named 1N0H_compound1_docked.pdb. UNK1 refers to the docked compound 1, all other structures are labeled as in the original 1N0H.pdb file downloaded from RCSB protein databank www.pdb.org.
DOI: 10.5061/dryad.bb5t3
title: Data from: Complex transient dynamics of stage-structured populations in response to environmental changes

description: Stage structures of populations can have a profound influence on their
 dynamics. However, not much is known about the transient dynamics that
 follow a disturbance in such systems. Here we combined chemostat
 experiments with dynamical modeling to study the response of the
 phytoplankton species Chlorella vulgaris to press perturbations. From an
 initially stable steady state, we altered either the concentration or
 dilution rate of a growth-limiting resource. This disturbance induced a
 complex transient response—characterized by the possible onset of
 oscillations—before population numbers relaxed to a new steady state.
 Thus, cell numbers could initially change in the opposite direction of the
 long-term change. We present quantitative indexes to characterize the
 transients and to show that the dynamic response is dependent on the
 degree of synchronization among life stages, which itself depends on the
 state of the population before perturbation. That is, we show how
 identical future steady states can be approached via different transients
 depending on the initial population structure. Our experimental results
 are supported by a size-structured model that accounts for interplay
 between cell-cycle and population-level processes and that includes
 resource-dependent variability in cell size. Our results should be
 relevant to other populations with a stage structure including organisms
 of higher order.
description: RawDataThe compressed file contains all raw data of the chemostat populations collected within this study. Please, find a more detailed description in the ReadMe.txt file.
DOI: 10.5061/dryad.cr8sn
title: Data from: Interglacial genetic diversification of Moussonia deppeana (Gesneriaceae), a hummingbird-pollinated, cloud forest shrub in northern Mesoamerica

description: Recent empirical work on cloud forest-adapted species supports the role of
 both old divergences across major geographical areas and more recent
 divergences attributed to Pleistocene climate changes. The shrub Moussonia
 deppeana is distributed in northern Mesoamerica, with geographically
 disjunct populations. Based on sampling throughout the species range and
 employing plastid and nuclear markers, we (i) test whether the fragmented
 distribution is correlated with main evolutionary lineages, (ii)
 reconstruct its phylogeographical history to infer the history of cloud
 forest in northern Mesoamerica and (iii) evaluate a set of
 refugia/vicariance scenarios for the region and demographic patterns of
 the populations whose ranges expanded and tracked cloud forest conditions
 during the Last Glacial Maximum. We found a deep evolutionary split in M.
 deppeana about 6–3 Ma, which could be consistent with a Pliocene
 divergence. Comparison of variation in plastid and nuclear markers
 revealed several lineages mostly congruent with their isolated
 geographical distribution and restricted gene flow among groups. Results
 of species distribution modelling and coalescent simulations fit a model
 of multiple refugia diverging during interglacial cycles. The demographic
 history of M. deppeana is not consistent with an expanding–contracting
 cloud forest archipelago model during the Last Glacial Maximum. Instead,
 our data suggest that populations persisted across the geographical range
 throughout the glacial cycles, and experienced isolation and divergence
 during interglacial periods.
description: MAXENT
 dataData used for MAXENT
 analyses. The file contains the georeferenced records of Moussonia
 deppeana, 19 variables of climatic data for each record, and correlation
 matrix between climatic variables.IMa2 input
 fileInput file used in the
 Isolation with Migration analysis implemented in IMa2.IMa2.txtITS alignmentITS sequences alignment of Moussonia deppeana.ITS_alignment.fastaRPL32 alignmentrpl32 sequence alignment of Moussonia deppeanaRPL32_alignment.fasta