cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4b6d3
title: Data from: Phylogenomic analyses support traditional relationships within Cnidaria

description: Cnidaria, the sister group to Bilateria, is the most diverse group of
 animals in terms of morphology, lifecycles, ecology, and development. How
 this diversity originated and evolved is not well understood because
 phylogenetic relationships among major cnidarian lineages are unclear, and
 recent studies present contrasting phylogenetic hypotheses. Here, we use
 transcriptome data from 15 newly-sequenced species in combination with 26
 publicly available genomes and transcriptomes to assess phylogenetic
 relationships among major cnidarian lineages. Phylogenetic analyses using
 different partition schemes and models of molecular evolution, as well as
 topology tests for alternative phylogenetic relationships, support the
 monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade
 consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly
 of Hexacorallia is weak due to the equivocal position of Ceriantharia.
 Taken together, these results further resolve deep cnidarian
 relationships, largely support traditional phylogenetic views on
 relationships, and provide a historical framework for studying the
 evolutionary processes involved in one of the most ancient animal
 radiations.
description: Phylogenetic alignments,
 tree sets, and summary trees13 files corresponding
 to the multiple sequence alignments, partition files, tree sets (bootstrap
 replicates and post burn-in posterior probabilities), and summary trees
 (maximum-likelihood trees and majority rule consensus trees) for multiple
 phylogenetic analyses.Zapata_et_al_Cnidaria_DryadData.tar.gz
DOI: 10.5061/dryad.n20ms
title: Data from: Atmospheric N deposition alters co-occurrence, but not functional potential among saprotrophic bacterial communities

description: The use of co-occurrence patterns to investigate interactions between
 micro-organisms has provided novel insight into organismal interactions
 within microbial communities. However, anthropogenic impacts on microbial
 co-occurrence patterns and ecosystem function remain an important gap in
 our ecological knowledge. In a northern hardwood forest ecosystem located
 in Michigan, USA, 20 years of experimentally increased atmospheric N
 deposition has reduced forest floor decay and increased soil C storage.
 This ecosystem-level response occurred concomitantly with compositional
 changes in saprophytic fungi and bacteria. Here, we investigated the
 influence of experimental N deposition on biotic interactions among forest
 floor bacterial assemblages by employing phylogenetic and molecular
 ecological network analysis. When compared to the ambient treatment, the
 forest floor bacterial community under experimental N deposition was less
 rich, more phylogenetically dispersed and exhibited a more clustered
 co-occurrence network topology. Together, our observations reveal the
 presence of increased biotic interactions among saprotrophic bacterial
 assemblages under future rates of N deposition. Moreover, they support the
 hypothesis that nearly two decades of experimental N deposition can modify
 the organization of microbial communities and provide further insight into
 why anthropogenic N deposition has reduced decomposition, increased soil C
 storage and accelerated phenolic DOC production in our field experiment.
description: Full Subsampled OTU
 tableThis is the full
 subsampled OTU table from which all analyses were
 based.16S.ForFloor.0.03.subsample.OTU.table.txtAmbient "core community" OTU tablesubsampled OTU table representing the "core community" of plots exposed to ambient N deposition.16S.ForFloor.final.an.0.03.subsample.0.03.filter.0.03.subsample.sharedN Deposition "core community" OTU tablesubsampled OTU table containing the OTUs representing the "core community" of experimental plots exposed to experimental N deposition16S.ForFloor.final.an.0.03.subsample.0.03.filter.0.03.subsample.sharedmothur pipelinethis is the mothur pipeline used to generate the full OTU table.pipeline for submission
DOI: 10.5061/dryad.8444
title: Data from: Interpreting the estimated timing of migration events between hybridizing species

description: The question of whether speciation can occur in the presence of gene flow
 has long been a contentious one. However, measuring the amount and timing
 of gene flow remains challenging. The computer program IMA2 allows
 researchers to estimate the timing of migration events for each locus
 during analyses, and these estimates have been used to infer the timing of
 introgression and mode of speciation. We use simulated datasets to examine
 the degree to which gene flow timing estimates can be used for these
 purposes, and what demographic conditions and datasets may be most
 amenable to gene flow timing estimation. We find that the 90% highest
 posterior density (HPD) interval of gene flow timing is almost always
 substantially wider than the actual window of gene flow, and increasing
 the information content of the dataset in terms of number of loci, number
 of sequences sampled, or locus length (and thus number of variable sites)
 has little impact on the posterior distribution over the range of values
 we tested. Even when simulated gene flow only occurred over the most
 recent 0.01% of the species’ history, the HPD interval usually encompasses
 the inferred divergence time. Our results indicate that gene flow timing
 estimates made using the method currently implemented in IMA2 cannot
 reliably be used to make inferences about the timing of introgression
 between diverged species or to distinguish between speciation with gene
 flow and allopatric speciation followed by one or more episodes of gene
 flow.
description: MEC-10-1217.R1_dataZipped folder containing 126 data files formatted for the program IMa2 as well as a README file explaining data file organization. All data were simulated using the program MS.
DOI: 10.7927/7q5a-dc02
title: IPCC AR6 Synthesis Report SPM.5 (c): Global methane (CH4) emissions

description: Development of global methane (CH₄) emissions pathways consistent with implemented policies and mitigation strategies. The figure shows pathways with colored ranges denoting the 5th to 95th percentiles across models. The red range represents emissions pathways assuming policies that were implemented by the end of 2020, as well as the Nationally Determined Contributions (NDCs). The green range shows pathways limiting global warming to 2°C (&gt;67%), while the blue range shows pathways limiting warming to 1.5°C (&gt;50%) with no or limited overshoot. The black line depicts past emissions (2000–2015). The error bar in 2015 indicates the 5th to 95th percentile uncertainty range of non-harmonized emissions across pathways. The figure also includes a "net zero" line indicating the long-term goal for methane emissions reduction.
DOI: 10.5061/dryad.733s9
title: Data from: Does GST underestimate genetic differentiation from marker data?

description: The widely applied genetic differentiation statistics FST and GST have
 recently been criticized for underestimating differentiation when applied
 to highly polymorphic markers such as microsatellites. New statistics
 claimed to be unaffected by marker polymorphisms have been proposed and
 advocated to replace the traditional FST and GST. This study shows that
 GST gives accurate estimates and underestimates of differentiation when
 demographic factors are more and less important than mutations,
 respectively. In the former case, all markers, regardless of diversity
 (HS), have the same GST value in expectation and thus give replicated
 estimates of differentiation. In the latter case, markers of higher HS
 have lower GST values, resulting in a negative, roughly linear correlation
 between GST and HS across loci. I propose that the correlation coefficient
 between GST and HS across loci, rGH, can be used to distinguish the two
 cases and to detect mutational effects on GST. A highly negative and
 significant rGH, when coupled with highly variable GST values among loci,
 would reveal that marker GST values are affected substantially by
 mutations and marker diversity, underestimate population differentiation,
 and are not comparable among studies, species and markers. Simulated and
 empirical data sets are used to check the power and statistical behaviour,
 and to demonstrate the usefulness of the correlation analysis.
description: Simulation programs for
 Gst, Hs and correlationsThis zipped file
 contains two simulation programs (source code in Fortran 90/95, and
 Windows executables), user's guides and example input files. The
 programs can be used to simulate genotype data under different migration
 and mutation models, and to calculate Gst, Hs, and their correlation from
 the simulated genotype data.Simu.zipSeven empirical datasets for Gst and Hs correlation analysisThis zipped file contains seven published microsatellite and SNP datasets used in CoDiDi analysisEmpiricalData.zip
DOI: 10.5061/dryad.1g23q
title: Data from: Diagnostic value of transthoracic echocardiography in patients with coarctation of aorta: the Chinese experience in 53 patients studied between 2008 and 2012 in one major medical center

description: Although aortography is well known as the “gold standard” for the
 diagnosis of coarctation of aorta (CoA), the method is invasive, expensive
 and not readily accepted by some patients. Ultrasound diagnosis for CoA is
 non-invasive, inexpensive, readily accepted by every patient, and can be
 repeated as frequently as necessary. The purpose of this presentation is
 to evaluate the applicability of transthoracic echocardiography for the
 diagnosis of CoA. The echocardiographic appearances of 53 patients with
 CoA who had undergone surgery during a 5-year period from January 2008 to
 October 2012 were analyzed retrospectively, and the results were compared
 with findings at surgery. Fifty-three patients with CoA include six with
 isolated CoA and 47 of CoA associated with other cardiac anomalies. Of the
 53 operated patients, 48 were correctly diagnosed preoperatively by
 echocardiography, while two were misdiagnosed as interrupted aortic arch
 and the diagnosis were missed in three other patients. Thus the diagnostic
 accuracy rate was 90.6%, and the misdiagnosis rate was 9.4%. Preoperative
 echocardiographic evaluation offers very satisfactory anatomic assessment
 in most patients with CoA. It makes preoperative angiography unnecessary.
 Thus transthoracic echocardiography should be the first-line method for
 the diagnosis of coarctation of the aorta.
description: figureFigure
 S1Figure
 S2S3.
 FigFigure
 S3.aviS4.
 FigFigure
 S4.avi
DOI: 10.5061/dryad.845
title: Data from: When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders

description: Convergence, i.e., similarity between organisms that is not the direct
 result of shared phylogenetic history (and that may instead result from
 independent adaptations to similar environments), is a fundamental issue
 that lies at the interface of systematics and evolutionary biology.
 Although convergence is often cited as an important problem in
 morphological phylogenetics, there have been few well-documented examples
 of strongly supported and misleading phylogenetic estimates that result
 from adaptive convergence in morphology. In this article, we propose
 criteria that can be used to infer whether or not a phylogenetic analysis
 has been misled by convergence. We then apply these criteria in a study of
 central Texas cave salamanders (genus Eurycea). Morphological characters
 (apparently related to cave-dwelling habitat use) support a clade uniting
 the species E. rathbuni and E. tridentifera, whereas mitochondrial DNA
 sequences and allozyme data show that these two species are not closely
 related. We suggest that a likely explanation for the paucity of examples
 of strongly misleading morphological convergence is that the conditions
 under which adaptive convergence is most likely to produce strongly
 misleading results are limited. Specifically, convergence is most likely
 to be problematic in groups (such as the central Texas Eurycea) in which
 most species are morphologically very similar and some of the species have
 invaded and adapted to a novel selective environment.
description: Eurycea Allozyme Data
 SetEurycea-allozyme_8-27-02.htmEurycea Combined Data SetEurycea-combined-data_8-27-.htmEurycea DNA Data SetEurycea-DNA_8-27-02.htmEurycea DNA/SSR Data SetEurycea-DNA_SSR_8-27-02.htm
DOI: 10.5061/dryad.56m2g
title: Data from: Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing

description: We study genome-wide nucleotide diversity in three subspecies of extant
 chimpanzees using exome capture. After strict filtering, SNVs and indels
 were called and genotyped for &gt;50% of exons at a mean coverage of
 35x per individual. Central chimpanzees (P. t. troglodytes) are the most
 polymorphic (nucleotide diversity, θw= 0.0023 per site) followed by
 Eastern (P. t. schweinfurthii) chimpanzees (θw = 0.0016) and Western (P.
 t. verus) chimpanzees (θw = 0.0008). A demographic scenario of divergence
 without gene flow fits the patterns of autosomal synonymous nucleotide
 diversity well except for a signal of recent gene flow from Western into
 Eastern chimpanzees. The striking contrast in X-linked vs. autosomal
 polymorphism and divergence previously reported in Central chimpanzees is
 also found in Eastern and Western chimpanzees. We show that the direction
 of selection (DoS) statistic exhibits a strong non-monotonic relationship
 with the strength of purifying selection S, making it inappropriate for
 estimating S. We instead use counts in synonymous vs. non-synonymous
 frequency classes to infer the distribution of S coefficients acting on
 non-synonymous mutations in each subspecies. The strength of purifying
 selection we infer is congruent with the differences in effective sizes of
 each subspecies: Central chimpanzees are undergoing the strongest
 purifying selection followed by Eastern and Western chimpanzees. Coding
 indels show stronger selection against indels changing the reading frame
 than observed in human populations.
description: Zip archive VCF
 filesZip file containing the
 very last version of VCF file containing all SNPS called on the three
 subspecies of chimpanzees for our publicationSee READMEArchive_VCF_Dryad.zip
DOI: 10.5061/dryad.jd2cb
title: Data from: Near infrared spectroscopy (NIRS) predicts non-structural carbohydrate concentrations in different tissue types of a broad range of tree species

description: 1. The allocation of non-structural carbohydrates (NSCs) to reserves
 constitutes an important physiological mechanism associated with tree
 growth and survival. However, procedures for measuring NSC in plant tissue
 are expensive and time-consuming. Near-infrared spectroscopy (NIRS) is a
 high-throughput technology that has the potential to infer the
 concentration of organic constituents for a large number of samples in a
 rapid and inexpensive way based on empirical calibrations with chemical
 analysis. 2. The main objectives of this study were (i) to develop a
 general NSC concentration calibration that integrates various forms of
 variation such as tree species and tissue types and (ii) to identify
 characteristic spectral regions associated with NSC molecules. In total,
 180 samples from different tree organs (root, stem, branch, leaf)
 belonging to 73 tree species from tropical and temperate biomes were
 analysed. Statistical relationships between NSC concentration and NIRS
 spectra were assessed using partial least squares regression (PLSR) and a
 variable selection procedure (competitive adaptive reweighted sampling,
 CARS), in order to identify key wavelengths. 3. Parsimonious and accurate
 calibration models were obtained for total NSC (r2 of 0·91, RMSE of 1·34%
 in external validation), followed by starch (r2 = 0·85 and RMSE = 1·20%)
 and sugars (r2 = 0·82 and RMSE = 1·10%). Key wavelengths coincided among
 these models and were mainly located in the 1740–1800, 2100–2300 and
 2410–2490 nm spectral regions. 4. This study demonstrates the ability of
 general calibration model to infer NSC concentrations across species and
 tissue types in a rapid and cost-effective way. The estimation of NSC in
 plants using NIRS therefore serves as a tool for functional biodiversity
 research, in particular for the study of the growth–survival trade-off and
 its implications in response to changing environmental conditions,
 including growth limitation and mortality.
description: Script
 modelScript with the
 statistical analysis.info_samplesData used to data analysis in RNSC_dataData used to data analysis in Rspectra_dataData used to data analysis in R
DOI: 10.5061/dryad.4h462
title: Data from: Detection and polarization of introgression in a five-taxon phylogeny

description: When multiple speciation events occur rapidly in succession, discordant
 genealogies due to incomplete lineage sorting (ILS) can complicate the
 detection of introgression. A variety of methods, including the
 D-statistic (a.k.a. the “ABBA–BABA test”), have been proposed to infer
 introgression in the presence of ILS for a four-taxon clade. However, no
 integrated method exists to detect introgression using allelic patterns
 for more complex phylogenies. Here we explore the issues associated with
 previous systems of applying D-statistics to a larger tree topology, and
 propose new DFOIL tests as an integrated framework to infer both the taxa
 involved in and the direction of introgression for a symmetric five-taxon
 phylogeny. Using theory and simulations, we show that the DFOIL statistics
 correctly identify the introgression donor and recipient lineages, even at
 low rates of introgression. DFOIL is also shown to have extremely low
 false-positive rates. The DFOIL tests are computationally inexpensive to
 calculate and can easily be applied to phylogenomic data sets, both
 genome-wide and in windows of the genome. In addition, we explore both the
 principles and problems of introgression detection in even more complex
 phylogenies.
description: Simulated
 DataSimulated site pattern
 data files from ms used for DFOIL analysissample_data.zipdfoil analysis scriptmain analysis script, use --help for full optionsdfoil.pydfoil simulation scriptuse --help for full optionsdfoil_sim.pyDFOIL post-analysis summarization scriptsummarizes introgression window statistics, use --help for full optionsdfoil_analyze.py
DOI: 10.5061/dryad.32451
title: Data from: Deforestation and forest fragmentation in South Ecuador since the 1970s - losing a hotspot of biodiversity

description: Deforestation and fragmentation are major components of global change;
 both are contributing to the rapid loss of tropical forest area with
 important implications for ecosystem functioning and biodiversity
 conservation. The forests of South Ecuador are a biological ‘hotspot’ due
 to their high diversity and endemism levels. We examined the deforestation
 and fragmentation patterns in this area of high conservation value using
 aerial photographs and Aster satellite scenes. The registered annual
 deforestation rates of 0.75% (1976–1989) and 2.86% (1989–2008) for two
 consecutive survey periods, the decreasing mean patch size and the
 increasing isolation of the forest fragments show that the area is under
 severe threat. Approximately 46% of South Ecuador’s original forest cover
 had been converted by 2008 into pastures and other anthropogenic land
 cover types. We found that deforestation is more intense at lower
 elevations (premontane evergreen forest and shrubland) and that the
 deforestation front currently moves in upslope direction. Improved
 awareness of the spatial extent, dynamics and patterns of deforestation
 and forest fragmentation is urgently needed in biologically diverse areas
 like South Ecuador.
description: Land_cover_South_EcuadorThe file contains information about land cover of South Ecuador for the years 1976, 1989, 2008. The covers for the two first years were generated from aerial photographs and the cover for the last year (2008) was generated from aster satellite scenes.
DOI: 10.5061/dryad.8476
title: Data from: Taxonomic structure of the fossil record is shaped by sampling bias

description: Understanding biases that affect how species are partitioned into higher
 taxa is critical for much of palaeobiology, as higher taxa are commonly
 used to estimate species diversity through time. Using the deep-sea record
 of coccolithophorid microfossils over the last 150 million years (myr), we
 demonstrate that sampling and taxonomic effort are important drivers of
 the species/genus ratio. An unexpected two-stepped change in the ratio of
 species to genera over the last 150 myr correlates strongly with changes
 in both the number of deep-sea sites yielding coccolithophorids that have
 been studied and with the number of taxonomists who have published on
 those sections. While some limited biological signature from major
 extinction events can be recognized from changes in the species/genus
 ratio, the numbers of sites and the numbers of taxonomists combined
 explain some 82% of the observed variation over long periods of geological
 time. Such a strong correlation argues against using raw species/genus
 ratios to infer biological processes without taking sampling into account,
 and suggests that higher taxa cannot be taken as unbiased proxies for
 species diversity.
description: Data
 filesSQL queries of
 databaseDryadData.xls