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opencc-by-4.0Jun 2020View details →

Fe chemical speciation collected using trace metal rosette in the Southern Ocean during the austral summer of 2016/2017, on board the Antarctic Circumnavigation Expedition.

Dataset abstract Fe chemical speciation of filtered seawater data are presented in this dataset, resulting from samples collected from a trace metal rosette on board the Antarctic Circumnavigation Expedition (ACE). During the austral summer of 2016/2017, seawater samples were collected from the Atlantic and Indian Ocean sectors of the Southern Ocean and dissolved Fe concentration, iron-binding organic ligands concentration and the conditional stability constant of Fe’ are presented here. Dataset contents <ul> <li>ace_fe_chemical_speciation.csv, data file, comma-separated values</li> <li>figure1.pdf, metadata, portable document format</li> <li>data_file_header.txt, metadata, text</li> <li>README.txt, metadata, text</li> </ul> Dataset license This Fe chemical speciation dataset from ACE is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) whose full text can be found at https://creativecommons.org/licenses/by/4.0/

opencc-by-4.0Dec 2019View details →

Non-refractory particulate sulfate and chloride data from a time of flight aerosol chemical speciation monitor around the Southern Ocean in the austral summer of 2016/17, during the Antarctic Circumnavigation Expedition (ACE).

Dataset abstract The Antarctic Circumnavigation Expedition (ACE) campaign was conducted between 20th December 2016 and 19th March 2017. The time of flight aerosol chemical speciation monitor (ToF-ACSM, Aerodyne Research Inc.) was deployed. It is capable of providing 10-minute resolution chemical compositions of NR-PM1 (non-refractory particulate matter with aerodynamic diameter smaller than 1 µm), including sulphate, nitrate, ammonium and organics. Chloride is refractory and can only be measured qualitatively, that is relative changes in intensity are trustworthy while absolute concentrations are a clear underestimation, because most of the chloride is in refractory form as part of sea salt in the marine environment. Since this ACSM dataset was collected on the ship, the ship exhaust will occasionally interfere with the natural signal. Therefore data gaps exist. The overall concentrations of particulate organics, nitrate and ammonium remained low, mostly below detection limit, except during the polluted periods. Thus, we do not report these three components. Only sulphate can be retrieved as a quantitative variable from this dataset. This dataset provides limited information on the chemical composition of sub-micron non-refractory aerosol in the Southern Ocean and gives hints on potential sources. Chloride clearly reflects the contribution of sea salt to the aerosol population. This can be checked by relating the particulate chloride to wind speed (Landwehr et al., 2019; 10.5281/zenodo.3379590) and particles with large diameters (Schmale et al., 2019; 10.5281/zenodo.2636709). Particulate sulphate may originate from a variety of sources: sea salt (minor contribution), anthropogenic emissions and natural marine emissions of dimethylsulfide, which is converted to SO2 and sulphuric acid in the atmosphere and can subsequently partition into the particle phase via gas-phase or aqueous phase reactions (Schmale et al., 2019). Dataset contents <ul> <li>raw_chl_SO4_mz_55_57_manual_with_flags.csv, data file, comma-separated values</li> <li>README.txt, metadata, text</li> <li>data_file_header.txt, metadata, text</li> <li>calibration_info.csv, metadata, comma-separated values</li> </ul>

opencc-by-4.0Dec 2019View details →

Seawater dissolved chromium concentration, redox speciation, and stable isotope composition in the North Pacific Ocean

Dissolved seawater chromium concentrations, redox speciation, and stable isotope composition were measured on samples collected in the North Pacific Ocean. Samples were collected over diel cycles (2 for stations 1-5, 1 for station 6) on board the RV Kilo Moana cruise KM1713 from Seward Alaska to Honolulu Hawai’i. Sampling stations spanned the subarctic North Pacific (stations 1 & 2), the dynamic subarctic-subtropical convergence zone (stations 3 and 4) and the subtropical North Pacific (stations 5 and 6). Chromium was enriched from filtered samples by Mg(OH)2 co-precipitation and analyzed by MC-ICP-MS using either isotope dilution (Cr redox speciation) or double spike methodology.

opencc-by-4.0Oct 2023View details →

Patterns of Speciation in a Parapatric Pair of Saturnia Moths as Revealed by Target Capture

This is the dataset for the manuscript entitled Patterns of Speciation in a Parapatric Pair of Saturnia Moths as Revealed by Target Capture. This study helps in the delimitation of a parapatric pair of two species of moths in a complex distribution considering their evolutionary history with the help of the Target Capture method.

edi52/100

Chemical speciation of copper in a salt marsh estuary near Sapelo Island, Georgia

The concentrations of dissolved copper (Cud), copper-binding ligands, thiourea-type thiols and humic substances (HSCu) were measured in estuarine waters adjacent to Sapelo Island, Georgia, USA, on a monthly basis from April to December 2014. Here we present the seasonal cycle of copper speciation within the estuary and compare it to the development of an annually occurring bloom of ammonia oxidising archaea (AOA) Thaumarchaeota, which require copper for many enzymes. Two types of complexing ligands (L1 and L2) were found to dominate with mean complex stabilities (log K'CuL) of 14.5 and 12.8. Strong complexation resulted in lowering of the free cupric ion (Cu2+) concentration to femtomolar (fM) levels throughout the study and to sub-fM levels during the summer months. A Thaumarchaeota bloom during this period suggests that this organism manages to grow at very low Cu2+ concentrations. Correlation of the concentration of the L1 ligand class with a thiourea-type thiol and the L2 ligand class with HSCu provide convincing evidence for the identity of the ligands. Due to the stronger complex stability, 82 - 99 % of the copper was bound to L1. Thiourea-type thiols form strong Cu(I) species, suggesting that ~90% copper is present as Cu(I) in this region, upsetting the paradigm of its predominance as Cu(II). In view of the very low concentration of free copper (pCu >15 at the onset and during the bloom) and a reputedly high requirement for copper, it is likely that the Thaumarchaeota are able to access the thiol-bound copper directly.

openCustomJan 2020View details →

zenodo48/100

Robust framework and software implementation for fast speciation mapping

R script and raw data to test the sparse excitation energy XAS procedure.

opencc-by-4.0Mar 2020View details →

opencc-by-4.0Mar 2020View details →

Speciation through chromosomal fusion and fission in Lepidoptera

28 Mai 2020 Phylogenetic trees, the chromoSSE script and the input data for the chromoSSE models belonging to the publication "Speciation through chromosomal fusion and fission in Lepidoptera" doi 10.1098/rstb.2019.0539.  For more information, contact jurriaan.devos@unibas.ch or kay.lucek@unibas.ch. The zipped folder "trees" contains three posterior distributions of chronograms for each of 16 genera, based on a sample of 100 trees each. Each tree includes the outgroup taxon, and the ingroup-outgroup split was dated based on one of three strategies: - For the files named GENUS_tmax_pl.tre based on the reported maximum (oldest) age of the reported interval; - For the files named GENUS_tmed_pl.tre based on the reported median age; - For the files named GENUS_tmax_pl.tre based on the reported minimum (youngest) age of the reported interval. Note that the outgroups were pruned prior to diversification rate analysis. The median age files were used as input for the ChromoSSE analysis; all files were used an input for the analyses based on Brownian Motion. The file "chromoSSE.Rev" contains a script that runs the cromoSSE models. Inorder to use this script RevBayes needs to be installed. This can be done by using the link: https://revbayes.github.io/download. It can be run with the command line: $> rb chromoSSE.Rev --args 1 As a argument every number between 1 and 16 can be used. And represent a genera: 1 = Colias, 2 = Erebia, 3 = Eunica, 4 = Eurema, 5 = Heliconius, 6 = Ithomia, 7 = Lycaena, 8 = Lysandra, 9 = Memphis, 10 = Morpho, 11 = Oleria, 12 = Papilio, 13 = Pieris, 14 = Polyommatus, 15 = Pteronymia, 16 = Taygetis. The process runs automatically and generates MCMC outputfiles and stores them in the directory "output". Each tree that is analyzed returns three files: -The files named "GENUS.ChromoSSE_anc_statesX.log" logfile of the states; -The files named "GENUS.ChromoSSE_finalX.tree" tree output of the analysis; -The files named "GENUS.ChromoSSE_modelX.log" logfile of the model. The files can be easily accessed by using the software Tracer: https://beast.community/tracer The zipped folder "data" contains input files needed for the chromoSSE analysis. To run each analysis a tree "GENUS.pruned.trees" and a tsv-file "GENUS.pruned.states.tsv" with the number of chromosomes per species is needed. In the trees all species without a chromosom number were excluded.

opencc-by-4.0Nov 2023View details →

Sub-speciation processes of equids in the Iberian Peninsula: ecological strategies and refuge areas

Metrical raw data of teeth and bones of Equus caballus and Equus hydruntinus from Canyars (Catalunya, Spain) They document the publication : Uzunidis, Sanz, Daura, 2024, Sub-speciation processes of equids in the Iberian Peninsula: ecological strategies and refuge areas, Quaternary Science Reviews, 325, 108473. https://www.sciencedirect.com/science/article/abs/pii/S0277379123005218

opencc-by-4.0Nov 2024View details →

Aqueous geochemical measurements and speciation calculations with concurrent copper resistance gene counts from sediment metagenomes over a seasonal cycle from 2015 to 2016 on Silver Bow Creek and Blacktail Creek near Butte, MT

This dataset contains information from concurrently gathered geochemical and metagenomic samples collected from Silver Bow Creek and Blacktail Creek near Butte, MT (SBC/BC) during 2015 and 2016. SBC/BC is recovering from metal contamination related to extensive mining in the area. Full geochemical measurements, geochemical speciation calculations, and gene counts of sequences mapping to copper resistance genes using MG-RAST are included.

openmit-licenseFeb 2022View details →

EDGAR v5.0 emissions inventory speciated for the MOZART chemical mechanism

Emission inventories need to be adapted to be used in chemical transport models (CTMs). They usually need ad-hoc preprocessing based on the chemical mechanism used in the CTM, including speciation of non-methane volatile organic compounds (NMVOCs).  Here we provide monthly <a href="https://edgar.jrc.ec.europa.eu/index.php/dataset_ap50">EDGAR v5.0 </a> global  air  pollutant  emissions  for  the  year  2015,  speciated  for  the  <a href="https://gmd.copernicus.org/articles/3/43/2010/">MOZART</a>  chemical mechanism. The dataset is also ready to use in <a href="https://ruc.noaa.gov/wrf/wrf-chem/">WRF-Chem </a>atmospheric model with MOZART-MOSAIC options. Emission files are provided as individual NetCDF files for each pollutant containing anthropogenic sector emissions as individual variables. In the folder you will find: <ul> <li>edgarv5_MOZART_data.tar.gz:  EDGAR  v5.0  monthly  emissions  for  the  year  2015  (NetCDFformat), speciated for MOZART chemical mechanism.  Both total and individual sector emissions are included in each file. </li> <li>edgarv5_MOZART_MOSAIC.inp:  Input file for anthroemiss preprocessing tool for MOZART-MOSAIC options in WRF-Chem.</li> <li>technical_note_EDGARv5_MOZART.pdf : documentation.</li> </ul> These files are also ready-to be used in <a href="https://www2.acom.ucar.edu/wrf-chem/wrf-chem-tools-community">WRF-Chem anthro-emiss preprocessing  tool</a> with the MOZART-MOSAIC options. Accompanying code for preparing the dataset can be found at repository: <a href="https://doi.org/10.5281/zenodo.6145846">https://doi.org/10.5281/zenodo.6145846</a> For more detail, please refer to the technical documentation (technical_note_EDGARv5_MOZART.pdf).

opencc-by-4.0Jun 2019View details →

XRS carbon K-edge speciation mapping of an Eocene (ca. 53 Mya) ant entrapped in amber from Oise, France

XRS carbon K-edge speciation mapping of an Eocene (ca. 53 Mya) ant entrapped in amber from Oise, France

opencc-by-4.0Apr 2023View details →

Fire INventory from NCAR (FINN) v2.5(MODIS), MOZART VOC speciation

The Fire INventory from NCAR (FINN) provides daily global fire emissions at high spatial resolution. The FINN model uses satellite detection of active fires (thermal anomalies) and the land cover type to determine the emission estimates. These emission estimates are based on MODIS active fire detection. Other versions of FINNv2.5 use MODIS+VIIRS fire detections. Please find additional VOC speciations and gridded emissions files at: https://doi.org//10.5065/XNPA-AF09

opencc-zeroAug 2020View details →

Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species R. mendax that attacks blueberries. The responses of 57,857 single nucleotide polymorphisms in a diapause study on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three flies at a field site in Fennville, Michigan, USA. As anticipated, the apple race and R. mendax show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause experiment on R. mendax revealed compensatory mutations throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in Rhagoletis. The generality of this result is placed in the context of other similar systems.

opencc-zeroSep 2020View details →

Is sexual conflict a driver of speciation? a case study with a tribe of brush-footed butterflies

Understanding the evolutionary mechanisms governing the uneven distribution of species richness across the tree of life is a great challenge in biology. Scientists have long argued that sexual conflict is a key driver of speciation. This hypothesis, however, has been highly debated in light of empirical evidence. Recent advances in the study of macroevolution make it possible to test this hypothesis with more data and increased accuracy. In the present study, we use phylogenomics combined with four different diversification rate analytical approaches to test whether sexual conflict is a driver of speciation in brush-footed butterflies of the tribe Acraeini. The presence of sphragis, an external mating plug found in most species among Acraeini, was used as a proxy for sexual conflict. Diversification analyses statistically reject the hypothesis that sexual conflict is associated with shifts in diversification rates in Acraeini. This result contrasts with earlier studies and suggests that the underlying mechanisms driving diversification are more complex than previously considered. In the case of butterflies, natural history traits acting in concert with abiotic factors possibly play a stronger role in triggering speciation than does sexual conflict.

opencc-zeroDec 2018View details →

Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)

Aim: The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of 'supertramps', 'great speciators' and relictualization. Location: The Indo-Pacific, Australia, Asia and Africa. Taxon: Corvoid passerine birds. Methods: We constructed a new time-calibrated molecular phylogeny of the core Campephagidae (cuckoo-shrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non-independence. Results: The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo-Pacific, Australia, South-East Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated ('supertramps') or show strong differentiation of local populations ('great speciators'), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in 'great speciators' with intermediate levels of dispersal abilities (as per hand-wing index). Main conclusions: Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of 'supertramps', 'great speciators' and relictual paleo-endemics within the temporal stages of the taxon cycle.

Figure 2 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 2. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI sequence. OUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 4 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 4. Number of base changes of transition and tansversion vs corrected pairwide distance diagram for whole mitochondrial gene.

Figure 1 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 1. Simplified cicada timetree built by BEAST v1.X, applying a 1,534 bp in maximum COI sequence. Inserted figure: Base substitution rate (= ratemedian shown at each node; substitutions per siteper millionyear; s/s/ myr) vsage (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by an Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 3 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 3. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI and 874 bp 18S rRNA sequences. OUTswith isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximatecurve with its formulawas drawn by Excel function, with the intersection for the curve = 0.0114 s/s/myr, the rate median shown on Tracer. Note that this rate is a little slower than thatsolely of COI in Figures 1 and 2, reflecting slowerrate of 18S rRNAthan COI (see Osozawa et al. 2017a).