cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pc5j0
title: Data from: Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference

description: Phylogenetic inference is generally performed on the basis of multiple
 sequence alignments (MSA). Because errors in an alignment can lead to
 errors in tree estimation, there is a strong interest in identifying and
 removing unreliable parts of the alignment. In recent years several
 automated filtering approaches have been proposed, but despite their
 popularity, a systematic and comprehensive comparison of different
 alignment filtering methods on real data has been lacking. Here, we extend
 and apply recently introduced phylogenetic tests of alignment accuracy on
 a large number of gene families and contrast the performance of unfiltered
 versus filtered alignments in the context of single-gene phylogeny
 reconstruction. Based on multiple genome-wide empirical and simulated data
 sets, we show that the trees obtained from filtered MSAs are on average
 worse than those obtained from unfiltered MSAs. Furthermore, alignment
 filtering often leads to an increase in the proportion of well-supported
 branches that are actually wrong. We confirm that our findings hold for a
 wide range of parameters and methods. Although our results suggest that
 light filtering (up to 20% of alignment positions) has little impact on
 tree accuracy and may save some computation time, contrary to widespread
 practice, we do not generally recommend the use of current alignment
 filtering methods for phylogenetic inference. By providing a way to
 rigorously and systematically measure the impact of filtering on
 alignments, the methodology set forth here will guide the development of
 better filtering algorithms.
description: Supplementary materials
 (including SFig 1-33, STable 1)Accepted topologies and
 lists of species for species-tree discordance test, lists of species for
 minimum duplication test, supplementary table 1, and supplementary figures
 1 to 33.Supplementary tables and
 figures.pdfRaw data of enriched
 species discordance, minimum duplication test, and simulation
 studyAlignment and trees
 associated with enriched species-tree discordance test, minimum
 duplication test, and simulation study.rawData.zipRaw data of Ensembl Compara analysesAlignment and trees associated with Ensembl compara data and pipeline.filtering_comparaRaw.tar.gzGenome listList of genomes used in the study, including source and release number.filtering_species.txt
DOI: 10.5061/dryad.2dc8k
title: Data from: European sea bass show behavioural resilience to near-future ocean acidification

description: Ocean acidification (OA)—caused by rising concentrations of carbon dioxide
 (CO2)—is thought to be a major threat to marine ecosystems and has been
 shown to induce behavioural alterations in fish. Here we show behavioural
 resilience to near-future OA in a commercially important and migratory
 marine finfish, the Sea bass (Dicentrarchus labrax). Sea bass were raised
 from eggs at 19°C in ambient or near-future OA (1000 µatm pCO2) conditions
 and n = 270 fish were observed 59–68 days post-hatch using automated
 tracking from video. Fish reared under ambient conditions, OA conditions,
 and fish reared in ambient conditions but tested in OA water showed
 statistically similar movement patterns, and reacted to their environment
 and interacted with each other in comparable ways. Thus our findings
 indicate behavioural resilience to near-future OA in juvenile sea bass.
 Moreover, simulated agent-based models indicate that our analysis methods
 are sensitive to subtle changes in fish behaviour. It is now important to
 determine whether the absences of any differences persist under more
 ecologically relevant circumstances and in contexts which have a more
 direct bearing on individual fitness.
description: Experimental
 DataThe x, y coordinates for
 fish in groups of n=10, at temporal resolution of 25 Hz (i.e. the frame
 rate).ESM_ExperimentalData.matSimulated DataThe x, y coordinates for simulated fish in groups of n=10, derived from the agent-based model.ESM_SimulatedData.mat
DOI: 10.5061/dryad.310q3
title: Data from: Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting

description: Species tree estimation is complicated by processes, such as gene
 duplication and loss and incomplete lineage sorting (ILS), that cause
 discordance between gene trees and the species tree. Furthermore, while
 concatenation, a traditional approach to tree estimation, has excellent
 performance under many conditions, the expectation is that the best
 accuracy will be obtained through the use of species tree estimation
 methods that are specifically designed to address gene tree discordance.
 In this paper, we report on a study to evaluate MP-EST – one of the most
 popular species tree estimation methods designed to address ILS – as well
 as concatenation under maximum likelihood, the greedy consensus, and two
 supertree methods (MRP and MRL). Our study shows that several factors
 impact the absolute and relative accuracy of methods, including the number
 of gene trees, the accuracy of the estimated gene trees, and the amount of
 ILS. Concatenation can be more accurate than the best summary methods in
 some cases (mostly when the gene trees have poor phylogenetic signal or
 when the level of ILS is low), but summary methods are generally more
 accurate than concatenation when there are an adequate number of
 sufficiently accurate gene trees. Our study suggests that coalescent-based
 species tree methods may be key to estimating highly accurate species
 trees from multiple loci.
description: Supplementary Online
 MaterialThis files includes
 supplementary material, including extra set of results, the model species
 trees used for simulation (as pdf), and the description of the exact
 commands used in the simulation study.Mirarab2014-SOM.pdfSimulated mammals - alignmentsSimulated sequence data (fasta files) corresponding to true gene trees simulated on the mammalian dataset.sequencedata.zipSimulated mammals - model species tree, true gene trees, and estimated species treesA simulated dataset based on Song et al 2012 mammals phylogeny. This file includes model species tree, true gene trees, and estimated species trees. Refer to the other zip files for estimated gene trees and sequence data. This is the corrected version.simulated-mammals.zipSimulated mammals - estimated gene treesEstimated gene trees on the simulated mammals dataset. All the 200 bootstrap replicates and the maximum likelihood gene trees are given for all model conditions studied in the paper. All gene trees are estimated using RAxML.genetrees.zipBiologicalBiological datasets. For Song et al 2012 biological dataset, gene trees, in addition to MRL and MP-EST species trees are included.biological-mammals.zip
DOI: 10.5061/dryad.5606t
title: Data from: Resources for phylogenomic analyses of Australian terrestrial vertebrates

description: High-throughput sequencing methods promise to improve our ability to infer
 the evolutionary histories of lineages and to delimit species. These are
 exciting prospects for the study of Australian vertebrates, a group
 comprised of many globally unique lineages with a long history of
 isolation. The evolutionary relationships within many of these lineages
 have been difficult to resolve with small numbers of loci, and we now know
 that many lineages also exhibit substantial cryptic diversity. Here, we
 present a set of phylogenetically diverse transcriptome resources to
 enable exon-based sequence capture studies of Australian vertebrates,
 including transcriptome sequences for four species of birds, four frogs,
 seven lizards and seven mammals. We also use exon data from the marsupial
 transcriptomes we generated to examine an approach for choosing a moderate
 number (dozens or hundreds) of phylogenetically informative exons based on
 a single transcriptome sequence, and a relatively distant reference
 genome.
description: Codecode.zipDatadata.zipREADMEA file containing a detailed description of the contents of this archive.
DOI: 10.5061/dryad.32j7r
title: Data from: Comparative authentication of Hypericum perforatum herbal products using DNA metabarcoding, TLC and HPLC-MS

description: Many herbal products have a long history of use, but there are increasing
 concerns over product efficacy, safety and quality in the wake of recent
 cases exposing discrepancies between labeling and constituents. When it
 comes to St. John’s wort (Hypericum perforatum L.) herbal products, there
 is limited oversight, frequent off-label use and insufficient monitoring
 of adverse drug reactions. In this study, we use amplicon metabarcoding
 (AMB) to authenticate 78 H. perforatum herbal products and evaluate its
 ability to detect substitution compared to standard methods using
 thin-layer chromatography (TLC) and high performance liquid chromatography
 coupled with mass spectrometry (HPLC-MS). Hypericum perforatum was
 detected in 68% of the products using AMB. Furthermore, AMB detected
 incongruence between constituent species and those listed on the label in
 all products. Neither TLC nor HPLC-MS could be used to unambiguously
 identify H. perforatum. They are accurate methods for authenticating
 presence of the target compounds, but have limited efficiency in detecting
 infrageneric substitution and do not yield any information on other plant
 ingredients in the products. Random post-marketing AMB of herbal products
 by regulatory agencies could raise awareness among consumers of
 substitution and would provide an incentive to manufacturers to increase
 quality control from raw ingredients to commercialized products.
description: Raclariu et
 al_2017_FASTQ Raw
DOI: 10.5061/dryad.tk569
title: Data from: Know your farmer: ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

description: Bark and ambrosia beetles are highly specialized weevils (Curculionidae)
 that have established diverse symbioses with fungi, most often from the
 order Ophiostomatales (Ascomycota, Sordariomycetes). The two types of
 beetles are distinguished by their feeding habits and intimacy of
 interactions with their symbiotic fungi. The tree tissue diet of bark
 beetles is facilitated by fungi, while ambrosia beetles feed solely on
 fungi that they farm. The farming life history strategy requires
 domestication of a fungus, which the beetles consume as their sole food
 source. Ambrosia beetles in the subfamily Platypodinae originated in the
 mid-Cretaceous (119-88Mya) and are the oldest known group of farming
 insects. However, attempts to resolve phylogenetic relationships and the
 timing of domestication events for fungal cultivars have been largely
 inconclusive. We sequenced the genomes of 12 ambrosia beetle fungal
 cultivars and bark beetle associates, including the devastating laurel
 wilt pathogen, Raffaelea lauricola, to estimate a robust phylogeny of the
 Ophiostomatales. We find evidence for contemporaneous diversification of
 the beetles and their associated fungi, followed by three independent
 domestication events of the ambrosia fungi genus Raffaelea. We estimate
 the first domestication of an Ophiostomatales fungus occurred ~86Mya, 25
 million years earlier than prior estimates and in close agreement with the
 estimated age of farming in the Platypodinae (96Mya). Comparisons of the
 timing of fungal domestication events with the timing of beetle radiations
 support the hypothesis that the first large beetle radiations may have
 spread domesticated ‘ambrosia’ fungi to other fungi-associated beetle
 groups, perhaps facilitating the evolution of new farming lineages.
description: SuperMatrix 22taxa
 978,795 amino acidsThis is a phylip
 formatted file of 22 taxa consisting of 2,207 concatenated amino acid
 sequences from single copy orthologs.22Oph.2207loci.CONCAT.phyAll_2207_aligned_loci.tar2,207 aligned loci, amino acid sequences, in fasta format used to construct Supertree86tax.Align86 taxa including Affroraffaelea with 3 genes for most taxa: SSU, LSU, Btub. I included an alignment of EF1alpha and RPB2 for ~23 genomes which would serve as an excellent resource for building primers for these genes in this group of fungi.86tax_8PartitionsData partitions for 86 taxa alignment in RAxML formatFunc_annotation.gff_Prot.fa_Transcripts.faCompressed protein, transcript, and general feature files for 15 annotated genomes. 12 sequenced this study, 3 previously published genomes.Dryad_Prots_Trans_Gff.tar.gzNewick formatted whole genome tree from Figure 1This is three in Figure 1, in newick format for use as a constraint tree in further analyses (86taxa alignment file).22tax.2200Loci.Genomes_IQMLtree.tre
DOI: 10.5061/dryad.3k502
title: Data from: A century of sprawl in the United States

description: The urban street network is one of the most permanent features of cities.
 Once laid down, the pattern of streets determines urban form and the level
 of sprawl for decades to come. We present a high-resolution time series of
 urban sprawl, as measured through street network connectivity, in the
 United States from 1920 to 2012. Sprawl started well before private car
 ownership was dominant and grew steadily until the mid-1990s. Over the
 last two decades, however, new streets have become significantly more
 connected and grid-like; the peak in street-network sprawl in the United
 States occurred in ∼1994. By one measure of connectivity, the mean nodal
 degree of intersections, sprawl fell by ∼9% between 1994 and 2012. We
 analyze spatial variation in these changes and demonstrate the persistence
 of sprawl. Places that were built with a low-connectivity street network
 tend to stay that way, even as the network expands. We also find
 suggestive evidence that local government policies impact sprawl, as the
 largest increases in connectivity have occurred in places with policies to
 promote gridded streets and similar New Urbanist design principles. We
 provide for public use a county-level version of our street-network sprawl
 dataset comprising a time series of nearly 100 y.
description: Barrington-Leigh-Millard-Ball-PNAS2015-Century-of-sprawl-graphs-in-GML-formatRoad network (graph) files in GML format. Numerous files (one per metro region) are compressed with GNU gzip, and then combined with GNU tar, and again compressed with GNU gzip.graphs-gml-format.tgzBarrington-Leigh-Millard-Ball-PNAS2015-Century-of-sprawl-shapefilesA collection of geographic information files in ESRI SHP format ("shapefiles"), one for each geographic level (state, metro and country), combined in ZIP format.Barrington-Leigh-Millard-Ball-PNAS2015-Century-of-sprawl-geographic-tabularGeographic tabular data in tab-separated text format (.tsv) and Python Pandas format (.pandas), for both stocks and time series, at several spatial scales, combined together using ZIP format.
DOI: 10.5061/dryad.78622
title: Data from: A simple biophysical model emulates budding yeast chromosome condensation

description: Mitotic chromosomes were one of the first cell biological structures to be
 described, yet their molecular architecture remains poorly understood. We
 have devised a simple biophysical model of a 300 kb-long nucleosome chain,
 the size of a budding yeast chromosome, constrained by interactions
 between binding sites of the chromosomal condensin complex, a key
 component of interphase and mitotic chromosomes. Comparisons of
 computational and experimental (4C) interaction maps, and other
 biophysical features, allow us to predict a mode of condensin action.
 Stochastic condensin-mediated pairwise interactions along the nucleosome
 chain generate native-like chromosome features and recapitulate chromosome
 compaction and individualization during mitotic condensation. Higher order
 interactions between condensin binding sites explain the data less well.
 Our results suggest that basic assumptions about chromatin behavior go a
 long way to explain chromosome architecture and are able to generate a
 molecular model of what the inside of a chromosome is likely to look like.
description: Condensation of a single
 chromatin chain in the Type I modelThe movie shows the full
 length of simulated chromosome condensation. Nucleosomes are shown as grey
 spheres, condensin binding sites are in red. If more than two condensin
 binding sites come within 40 nm of each other, they are highlighted by a
 yellow sphere to indicate ‘rosette’ formation. Chromatin loops that
 connect condensin binding sites within rosettes are tinted cyan. A
 balanced co-existence of rosette and web-like structures in the compacted
 mitotic stage becomes apparent.single_chain_type_I.mp4Condensation of a single chromatin chain in the Type II modelAs previous movie, but the simulation followed the Type II model. Now the rosette-like topologies become dominant and the overall structure is densely packed.single_chain_type_II.mp4Condensation of two nearby chromatin chains in the Type I modelFull length movie of two chromatin chains compacting next to each other using the Type I model are shown, illustrating chain separation during condensation (chain 1, nucleosomes in light blue, condensin binding sties in red; chain 2, nucleosomes in yellow, condensin binding sites in green).two_chains_type_I.mp4Condensation of two nearby chromatin chains in the Type II modelAs previous movie, but using the Type II model. The two chromatin chains fail to separate during condensation.two_chains_type_II.mp4
DOI: 10.5061/dryad.75b30
title: Data from: Dispersal enhances beta diversity in nectar microbes

description: Dispersal is considered a key driver of beta diversity, the variation in
 species composition among local communities, but empirical tests remain
 limited. We manipulated dispersal of nectar-inhabiting bacteria and yeasts
 via flower-visiting animals to examine how dispersal influenced microbial
 beta diversity among flowers. Contrary to the prevailing view that
 dispersal lowers beta diversity, we found beta diversity was highest when
 dispersal was least limited. Our analysis suggested that this unexpected
 pattern might have resulted from stronger priority effects under increased
 dispersal. Dispersal is highly stochastic, generating variability in
 species arrival history and consequently the potential for community
 divergence via priority effects, in these and likely many other microbial,
 plant, and animal communities. Yet most previous experiments eliminated
 this possibility. We suggest that the positive effects of dispersal on
 beta diversity, like the one we report here, may have been greatly
 underappreciated.
description: Field data for Figure
 5csv
 file of sample flower ID, proportion of nectar sugars monosaccharides
 (glucose+fructose)/(glucose+fructose+sucrose), flower treatment, Log10
 Bacterial Colony Forming Units (CFUs), Log10 Fungal CFUs, PCoA of
 Bacterial community composition based on Bray-Curtis
 dissimilarities.FieldSurvey_CFUS&Sugars.csvBacterial_OTU_tableBacterial OTU Table for ordinations, beta diversity and beta deviation calculationsData_for_bacterial_OTUsMetadata including flower or bird ID and flower treatment for bacterial community data (OTU table).Nectar_fungi_seqRaw ITS (Fungal) sequence reads from the nectar of Mimulus aurantiacusNectar_bacteria_seqRaw 16S (Bacterial) sequence reads from the nectar of Mimulus aurantiacusBacterial_seq.zip
DOI: 10.5281/zenodo.18380319
title: Potential use of Sargassum muticum as source of plant biostimulants after three different drying methods
DOI: 10.5061/dryad.22qc2
title: Data from: Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet

description: Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa.
 Farmers usually grow varieties with different cycle lengths and
 complementary functions in Sahelian agrosystems. Both the level of genetic
 differentiation of these varieties and the domestication history of pearl
 millet have been poorly studied. We investigated the neutral genetic
 diversity and population genetic structure of early- and late-flowering
 domesticated and wild pearl millet populations using 18 microsatellite
 loci and 8 nucleotide sequences. Strikingly, early- and late-flowering
 domesticated varieties were not differentiated over their whole
 distribution area, despite a clear difference in their
 isolation-by-distance pattern. Conversely, our data brought evidence for
 two well-differentiated genetic pools in wild pearl millet, allowing us to
 test scenarios with different numbers and origins of domestication using
 approximate Bayesian computation (ABC). The ABC analysis showed the likely
 existence of asymmetric migration between wild and domesticated
 populations. The model choice procedure indicated that a single
 domestication from the eastern wild populations was the more likely
 scenario to explain the polymorphism patterns observed in cultivated pearl
 millet.
description: Polymorphism
 dataMicrosatellite and
 nucleotide sequence data sets, used in the polymorphism study and the ABC
 analysis. ReadMe files describing the data are included in the
 directories.Polymorphism_data.zipScripts and reference tables of the ABC analysisContains the scripts needed to perform the simulations with ABCtoolbox and fastsimcoal for the ABC analysis, and the reference tables for each simulated model. ReadMe files are included in the directories.ABC.zip
DOI: 10.5281/zenodo.18380318
title: Potential use of Sargassum muticum as source of plant biostimulants after three different drying methods
DOI: 10.5061/dryad.5p6vv
title: Data from: Evolutionary suppression of erythropoiesis via the modulation of TGF-β signaling in an Antarctic icefish

description: The Antarctic icefish, a family (Channichthyidae) of teleosts within the
 perciform suborder Notothenioidei, are the only known vertebrates without
 oxygen-transporting haemoglobins and that are largely devoid of
 circulating erythrocytes. To elucidate the evo-devo mechanisms
 underpinning the suppressed erythropoiesis in the icefish, we conducted
 comparative studies on the transcriptomes and microRNAomes of the primary
 haematopoietic tissues between an icefish (Chionodraco hamatus) and two
 red-blooded notothenioids (Trematomus bernacchii and Gymnodraco
 acuticeps). We identified substantial remodelling of the haematopoietic
 programs in the icefish through which erythropoiesis is selectively
 suppressed. Experimental verification showed that erythropoietic
 suppression in the icefish may be attributable to the upregulation of
 TGF-β signalling, which coincides with reductions in multiple
 transcription factors essential for erythropoiesis and the upregulation of
 hundreds of microRNAs, the majority (&gt; 80%) of which potentially
 target erythropoiesis regulating factors. Of the six microRNAs selected
 for verification, three miRNAs (miR-152, miR-1388 and miR-16b)
 demonstrated suppressive functions on GATA1 and ALAS2, which are two
 factors important for erythroid differentiation, resulting in reduced
 numbers of erythroids in microinjected zebra fish embryos. Codon
 substitution analyses of the genes of the TGF-β superfamily revealed signs
 of positive selection in TGF-β1 and endoglin in the lineages leading to
 Antarctic notothenioids. Both genes are previously known to function in
 erythropoietic suppression. These findings implied a general trend of
 erythropoietic suppression in the cold-adapted notothenioid lineages
 through evolutionary modulation of the multi-functional TGF-β signalling
 pathway. This trend is more pronounced in the haemoglobin-less icefish,
 which may pre-emptively hinder the otherwise defective erythroids from
 production.
description: DRYAD_Supplemental
 Data