cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2k9j0
title: Data from: Low-parameter phylogenetic inference under the general Markov model

description: In their 2008 and 2009 papers, Sumner and colleagues introduced the
 "squangles" -- a small set of Markov invariants for phylogenetic
 quartets. The squangles are consistent with the general Markov model (GM)
 and can be used to infer quartets without the need to explicitly estimate
 all parameters. As GM is inhomogeneous and hence non-stationary, the
 squangles are expected to perform well compared to standard approaches
 when there are changes in base-composition amongst species. However, the
 GM model assumes constant rates across sites, so the squangles should be
 confounded by data generated with invariant sites or other forms of
 rate-variation across sites. Here we implement the squangles in a
 least-squares setting that returns quartets weighted by either confidence
 or internal edge lengths, and we show how these weighted quartets can be
 used as input into a variety of supertree and supernetwork methods. For
 the first time, we quantitatively investigate the robustness of the
 squangles to breaking of the constant rates-across-sites assumption on
 both simulated and real data sets; and we suggest a modification that
 improves the performance of the squangles in the presence of invariant
 sites. Our conclusion is that the squangles provide a novel tool for
 phylogenetic estimation that is complementary to methods that explicitly
 account for rate-variation across sites, but rely on homogeneous -- and
 hence stationary -- models.
description: Complete Simulation
 ResultsThis excel spreadsheet
 gives the complete simulation results for all methods and parameter
 settings described in the main simulation.completeSimulationResults.xlsxSquangle Python CodeThis zip files includes the python implementation of the squangles method, the files that define the squangle polynomials, an example input file, and example output file and a README file that describes how to use the code.SquangleCode.zip
DOI: 10.5061/dryad.p4356
title: Data from: Selection on variance-controlling genes – adaptability or stability

description: Simulations on a model system where a variance-controlling master locus
 scales the effects of a set of effector loci show that selection affects
 the variance-controlling locus more strongly than the effector loci, and
 that the direction of selection is dependent on the frequency of
 environmental changes.
description: Supp2_simulation_resultsThe complete raw data underlying all graphs and tables shown in the article. All data were produced using the simulation code that constitutes the other supplementary zip-archive.Supp1_simulation_codeThe JAVA source code used for the simulations described in the article.
DOI: 10.5061/dryad.099s2
title: Data from: Detecting the footprints of divergent selection in oaks with linked markers

description: Genome scans are increasingly used to study ecological speciation,
 providing a useful genome-wide perspective on divergent selection in the
 presence of gene flow. Here, we compare current approaches to detect
 footprints of divergent selection in closely related species. We analyzed
 192 individuals from two interfertile European temperate oak species using
 30 genomic microsatellites from eight linkage groups. These markers
 present little intraspecific differentiation and can be used in
 combination to assign individual genotypes to species. We first show that
 different outlier detection tests give somewhat different results,
 possibly due to model constraints. Second, using linkage information for
 these markers, we further characterize the signature of divergent
 selection in the presence of gene flow. In particular, we show that
 recombination estimates for regions with outlier markers are lower than
 those for a control region, in line with a prediction from ecological
 speciation theory. Most importantly, we show that analyses at the
 haplotype level can distinguish between truly divergent (bi-directional)
 selection and positive selection in one of the two species, offering a new
 and improved method for characterizing the speciation process.
description: Data_01_HDY_11_OR0383RRGenotypes for 192 trees at 30 nSSRs. Stand locations. Morphological classification for each tree.Supp01_HDY_11_OR0383RRSupplementary information for the analyses carried out with the software StructureSupp02_HDY_11_OR0383RRSupplemental information for the genetic diversity and differentiation statistics.Supp03_HDY_11_OR0383RRSupplemental information for the tests carried out to detect selective sweeps.Supp04_HDY_11_OR0383RRSupplemental information for the haplotype inferences with Phase and with the ELB algorithm.Supp05_HDY_11_OR0383RRSupplemental information for the convergence diagnostic tests of the posterior distributions from Phase haplotype inferences and recombination estimates.Supp06_HDY_11_OR0383RRSupplemental information for the linkage disequilibrium estimates.
DOI: 10.5061/dryad.4rq51
title: Data from: Independent FLC mutations as causes of flowering time variation in Arabidopsis thaliana and Capsella rubella

description: Capsella rubella is an inbreeding annual forb closely related to
 Arabidopsis thaliana, a model species widely used for studying natural
 variation in adaptive traits such as flowering time. Although mutations in
 dozens of genes can affect flowering of A. thaliana in the laboratory,
 only a handful of such genes vary in natural populations. Chief among
 these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI
 mutations along with rare FLC mutations explain a large fraction of
 flowering-time variation in A. thaliana. Here we document flowering time
 under different conditions in 20 C. rubella accessions from across the
 species' range. Similar to A. thaliana, vernalization, long
 photoperiods and elevated ambient temperature generally promote flowering.
 In this collection of C. rubella accessions, we did not find any obvious
 loss-of-function FRI alleles. Using mapping-by-sequencing with two strains
 that have contrasting flowering behaviors, we identified a splice-site
 mutation in FLC as the likely cause of early flowering in accession 1408.
 However, other similarly early C. rubella accessions did not share this
 mutation. We conclude that the genetic basis of flowering-time variation
 in C. rubella is complex, despite this very young species having undergone
 an extreme genetic bottleneck when it split from C. grandiflora a few tens
 of thousands of years ago.
description: SNPs in accession
 1408SNPs in accession 1408
 identified by whole-genome resequencingGuo_table_S2.txt.gzDifferences between accession 1408 and reference accession MTE in final mapping intervalVariants were called with SHORE v0.8 and pindel v0.2.4s. The FLC gene model is highlighted in bold and red.Guo_table_S4.xlsx
DOI: 10.5258/soton/d3825
title: Dataset for Towards Low-Frequency Acoustic sensing using Antiresonant Hollow-Core Fibers

description: This dataset supports the manuscript under review on Photonics Research:
Meng Ding, William Luocheng Wu, Thomas William Kelly, Gregory T. Jasion, Ian A. Davidson, Ali Masoudi, Paul White, Francesco Poletti and Radan Slavik, "Towards Low-Frequency Acoustic sensing using Antiresonant Hollow-Core Fibers," in Photonics Research.
DOI: 10.15468/zvmmvn
title: San Francisco State University, Harry D. Thiers Herbarium

description: The primary research focus of the Harry D. Thiers Herbarium is mycology. Most of the early collections were made by Harry Thiers and his students, and later by Dennis Desjardin and his students. Specialties include fleshy fungi of North America, Hawai'i, Indonesia, and southeast Asia; California lichens, bryophytes, and flowering plants, with an exceptionally large collection of Arctostaphylos. The herbarium was established in 1959 as the SFSU Herbarium, and was renamed the HDT Herbarium following Harry's retirement in 1989.
DOI: 10.5061/dryad.q8f74
title: Data from: A jungle in there: bacteria in belly buttons are highly diverse, but predictable

description: The belly button is one of the habitats closest to us, and yet it remains
 relatively unexplored. We analyzed bacteria and arachaea from the belly
 buttons of humans from two different populations sampled within a
 nation-wide citizen science project. We examined bacterial and archaeal
 phylotypes present and their diversity using multiplex pyrosequencing of
 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from
 tropical macroecology, namely that the frequency of phylotypes in one
 sample of humans predicts its frequency in another independent sample. We
 also tested the predictions that frequent phylotypes (the oligarchs) tend
 to be common when present, and tend to be more phylogenetically clustered
 than rare phylotypes. Once rarefied to four hundred reads per sample,
 bacterial communities from belly buttons proved to be at least as diverse
 as communities known from other skin studies (on average 67 bacterial
 phylotypes per belly button). However, the belly button communities were
 strongly dominated by a few taxa: only 6 phylotypes occurred on
 &gt;80% humans. While these frequent bacterial phylotypes (the archaea
 were all rare) are a tiny part of the total diversity of bacteria in human
 navels (&lt;0.3% of phylotypes), they constitute a major portion of
 individual reads (~1/3), and are predictable among independent samples of
 humans, in terms of both the occurrence and evolutionary relatedness (more
 closely related than randomly drawn equal sets of phylotypes). Thus, the
 hypothesis that “oligarchs” dominate diverse assemblages appears to be
 supported by human-associated bacteria. Although it remains difficult to
 predict which species of bacteria might be found on a particular human,
 predicting which species are most frequent (or rare) seems more
 straightforward, at least for those species living in belly buttons.
description: belly buttons ordination
 with labelsraw_seqs_BB.fnaBellyButton.Only_Mapping_FileAligned representative sequencesrep_set_BB_aligned.fas
DOI: 10.5061/dryad.9f3n1
title: Data from: Precipitation, soils, NPP, and biodiversity: resurrection of Albrecht's Curve

description: Climate and soils are widely recognized as major drivers of virtually all
 properties of ecosystems and communities. However, despite major advances
 in the understanding of soil formation and ecosystem dynamics, the effects
 of climate on soil properties are not widely appreciated. Understanding
 the effects of water availability on the rates of chemical and biological
 processes that affect soil formation can help clarify the global patterns
 of soil fertility, which affect agricultural and forest productivity, as
 well as biodiversity. Empirical tests of Albrecht's conceptual model
 of soil development and degradation using global climate and soil datasets
 and soil chronosequences confirm that soil total exchangeable bases (TEB),
 phosphorus, nitrogen and other components of soil fertility, along with
 plant productivity generally decline on older soils and under wetter
 conditions as precipitation exceeds potential evapotranspiration. The
 basic pattern of soil fertility in relation to water availability is a
 unimodal curve, with a maximum near or below a water balance of zero
 (annual precipitation - annual potential evapotranspiration). Analysis of
 global data by sub-regions reveals significant differences between
 temperate and tropical soil fertility distributions, as well as
 significant differences between continents. The low levels of soil
 nutrients (e.g., TEB, P, N) and plant productivity found on ancient soils
 or highly weathered soils in regions with high precipitation suggest that
 the positive effects of low productivity on plant diversity that have been
 observed at local and regional scales may also occur at the global scale.
description: Linux gzip tar file with
 large datafilesFilestoDryad.tar.gz
DOI: 10.5061/dryad.8v684
title: Data from: Long-term data reveal patterns and controls on streamwater chemistry in a forested stream: Walker Branch, Tennessee

description: We present 20 years of weekly streamwater chemistry, hydrology, and
 climate data for the Walker Branch watershed in eastern Tennessee, USA.
 Since 1989, the watershed has experienced a ~1.0˚C increase in mean annual
 temperature, a ~20% decline in precipitation, and a ~30% increase in
 forest evapotranspiration rates. As a result, runoff has declined by ~34%.
 We evaluate long-term trends in streamwater concentrations and fluxes for
 9 solutes and use wet deposition data to calculate approximate watershed
 input-output budgets. Dissolved constituents were classified as
 geochemical solutes (Ca2+, Mg2+ and SO42-) or nutrients (NH4+, NO3-, SRP,
 TSN, TSP, and DOC). Geochemical solutes are predominantly controlled by
 discharge and long-term changes in catchment hydrology have led to
 significant trends in the concentrations and fluxes of these solutes.
 Further, trends in geochemical solute concentrations indicate shifting
 soil flowpath contributions to streamflow generation through time, with
 deep groundwater having a greater proportional contribution in recent
 years. Despite dramatic changes in watershed runoff, there were no trends
 in inorganic nutrient concentrations (NH4+, NO3-, and SRP). While most
 nutrients entering the watershed are retained, stream fluxes of nutrient
 solutes have declined significantly as a result of decreasing runoff.
 Nutrient concentrations in streamwater exhibit large seasonality
 controlled by in-stream biological uptake. Stream benthic communities are
 sensitive to hydrologic disturbance and changes in the frequency or
 intensity of storm events through time can affect nutrient fluxes. Stream
 NO3- concentrations are also sensitive to drought, with concentrations
 decreasing (increasing) if conditions during the 3 years prior to the time
 of sampling were drier (wetter) than the long-term mean. Future changes in
 the incidence of storm events, as well as the number and duration of
 droughts, have the potential to significantly alter watershed nutrient
 losses. Our analysis indicates that changing climates can differentially
 affect watershed element cycles through changes in biogeochemical process
 rates or through changes in catchment hydrology. Furthermore, climate
 change can include both long-term trending in mean climate variables, as
 well as changes in the frequency and intensity of storms and droughts,
 with each of these types of change having distinct effects on biological
 and geochemical processes governing different solutes.
description: West WB longterm weekly
 chem data_sequential 1989 to 2008_4Mar09West WBW ave daily
 discharge_1989 to 2008
DOI: 10.5061/dryad.8q6n4
title: Data from: Genomic analysis of a key innovation in an experimental Escherichia coli population

description: Evolutionary novelties have been important in the history of life, but
 their origins are usually difficult to examine in detail. We previously
 described the evolution of a novel trait, aerobic citrate utilization
 (Cit+), in an experimental population of Escherichia coli. Here we analyze
 29 genomes to investigate the history and genetic basis of this trait. At
 least three distinct clades coexisted for more than 10,000 generations
 prior to its emergence. The Cit+ trait originated in one clade by a tandem
 duplication that captured an aerobically-expressed promoter for the
 expression of a previously silent citrate transporter. The clades varied
 in their propensity to evolve this novel trait, although genotypes able to
 do so existed in all three clades, implying that multiple potentiating
 mutations arose during the population’s history. Our findings illustrate
 the importance of promoter capture and altered gene regulation in
 mediating the exaptation events that often underlie evolutionary
 innovations.
description: Blount et al Nat 2012
 ExpressionBlount et al Nat 2012
 fig 4b rawBlount et al Nat 2012
 fig 4b transformedBlount et al Nat 2012
 fig 4c transformedBlount et al Nat 2012
 fig 5c rawBlount et al Nat 2012
 fig 5c transformedBlount et al Nat 2012
 fig 6a rawBlount et al Nat 2012
 fig 6a transformedBlount et al Nat 2012
 fig 6b rawBlount et al Nat 2012
 fig 6b transformedBlount et al Nat 2012
 fig 6c rawBlount et al Nat 2012
 fig 6c transformedBlount et al Nat 2012
 fig 6d rawBlount et al Nat 2012
 fig 6d transformedBlount et al Nat 2012
 sup fig 3 rawBlount et al Nat 2012
 sup fig 3 transformedBlount et al Nat 2012
 sup fig 5 set 1 rawBlount et al Nat 2012
 sup fig 5 set 1 transformedBlount et al Nat 2012
 sup fig 5 set 2 rawBlount et al Nat 2012
 sup fig 5 set 2 transformedBlount et al Nat 2012
 sup fig 5 set 3 rawBlount et al Nat 2012
 sup fig 5 set 3 transformedBlount et al Nat 2012
 fig 7
DOI: 10.5061/dryad.kc6m8
title: Data from: A gain-of-function polymorphism controlling complex traits and fitness in nature

description: Identification of the causal genes that control complex trait variation
 remains challenging, limiting our appreciation of the evolutionary
 processes that influence polymorphisms in nature. We cloned a quantitative
 trait locus that controls plant defensive chemistry, damage by insect
 herbivores, survival, and reproduction in the natural environments where
 this polymorphism evolved. These ecological effects are driven by
 duplications in the BCMA (branched-chain methionine allocation) loci
 controlling this variation and by two selectively favored amino acid
 changes in the glucosinolate-biosynthetic cytochrome P450 proteins that
 they encode. These changes cause a gain of novel enzyme function,
 modulated by allelic differences in catalytic rate and gene copy number.
 Ecological interactions in diverse environments likely contribute to the
 widespread polymorphism of this biochemical function.
description: BCMA fine
 mappingBCMA heterologous
 expressionBCMA2 genotypes &
 linkageCO endogenous leaf
 damageCO
 manipulativeGS
 transgenicsLab Boechera_East
 GSLab Boechera_East
 TniLab Data for Tni TotGS
 BCratio histogramMicrosatellite data 28
 loci from 9 populationsMT&CO Plant Means
 BC-ratioNILs 2008 BCMA GS
 TraitsNILs MT&CO
 HerbivoryParker x Ruby GS
 dataRILs MT&CO FamMeans
 BCMA nohetsRILs MT&CO indiv
 plants BCMA nohetsBCMA allele-specific
 expression
DOI: 10.5061/dryad.b68hr
title: Data from: Environmentally induced dispersal-related life history syndrome in the tropical butterfly, Bicyclus anynana

description: Dispersal is a key process for understanding the persistence of
 populations as well as the capacity of organisms to respond to
 environmental change. Therefore understanding factors that may facilitate
 or constrain the evolution of dispersal is of crucial interest.
 Assessments of phenotypic variation in various behavioural, physiological
 and morphological traits related to insect dispersal and flight
 performance are common, yet very little is known about the genetic
 associations among these traits. We have used experiments on the butterfly
 Bicyclus anynana to estimate genetic variation and co-variation in seven
 behavioural, physiological and morphological traits related to flight
 potential and hence dispersal. Our goal was to characterize the
 heritabilities and genetic correlations among these traits, and thus to
 understand more about the evolution of dispersal-related life-history
 syndromes in butterflies. Using a version of the animal-model, we showed
 that all of the traits varied between the sexes, and most were either
 positively or negatively (phenotypically and/or genetically) correlated
 with body size. Heritable variation was present in most traits, with the
 highest heritabilities estimated for body mass and thorax ratio. The
 variance of flight activity among multiple measurements for the same
 individual was high even after controlling for the prevailing
 environmental conditions, indicating the importance of behavioural
 switching and/or inherent randomness associated with movement. A number of
 dispersal-related traits showed phenotypic correlations among one another,
 but only a few of these were associated with significant genetic
 correlations indicating that co-variances between these traits in Bicyclus
 anynana are mainly environmentally induced.
description: Bicyclus
 data_Saastamoinen et al. 2012_JEBThe file data.xls
 includes all data needed to fit the animal model.MATHEMATICA6_estimateMATHEMATICA6_estimate.nb includes the source code needed to fit the model to data. It also illustrates the obtained parameter estimates and the mixing of the algorithm.MathLinkLDLThe file MathLinkLDL.exe is a linear solver that is called from the Mathematica file.
DOI: 10.5061/dryad.md023
title: Data from: Minimizing the average distance to a closest leaf in a phylogenetic tree

description: When performing an analysis on a collection of molecular sequences, it can
 be convenient to reduce the number of sequences under consideration while
 maintaining some characteristic of a larger collection of sequences. For
 example, one may wish to select a subset of high-quality sequences that
 represent the diversity of a larger collection of sequences. One may also
 wish to specialize a large database of characterized “reference sequences”
 to a smaller subset that is as close as possible on average to a
 collection of “query sequences” of interest. Such a representative subset
 can be useful whenever one wishes to find a set of reference sequences
 that is appropriate to use for comparative analysis of
 environmentally-derived sequences, such as for selecting “reference tree”
 sequences for phylogenetic placement of metagenomic reads. In this paper
 we formalize these problems in terms of the minimization of the Average
 Distance to the Closest Leaf (ADCL) and investigate algorithms to perform
 the relevant minimization. We show that the greedy algorithm is not
 effective, show that a variant of the Partitioning Among Medoids (PAM)
 heuristic gets stuck in local minima, and develop an exact dynamic
 programming approach. Using this exact program we note that the
 performance of PAM appears to be good for simulated trees, and is faster
 than the exact algorithm for small trees. On the other hand, the exact
 program gives solutions for all numbers of leaves less than or equal to
 the given desired number of leaves, while PAM only gives a solution for
 the pre-specified number of leaves. Via application to real data, we show
 that the ADCL criterion chooses chimeric sequences less often than random
 subsets, while the maximization of phylogenetic diversity chooses them
 more often than random. These algorithms have been implemented in publicly
 available software.
description: Files for validating the
 solutions given by the PAM and full implementations of the minimum ADCL
 algorithmvoronoi-validation.zipFiles for assessing the behavior of ADCL minimization under bootstrappingbootstrap.zipFiles for comparing performance of PAM and full implementations of the minimum ADCL algorithm on trees of varying sizen-complexity.zipFiles for assessing the behavior of ADCL algorithms with chimeric sequenceschimeras.zipFiles for evaluating PAM and full implementations of the minimum ADCL algorithm at various values of the parameter `k`k-complexity.zipSupplementary figuresvoro_suppfig.pdf