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openOpenDec 2015View details →

Radiocarbon dates for an elevational gradient by Toolik Lake, North Slope of Alaska 1988.

Two cores of peat, approximately 15 cm2, were cut to the depth at which mineral soils were encountered at each site. The sites of sampling correspond to an elevational gradient leading from the lakeside upslope to the begining of the water track at the ridgetop. Each sample was divided into three sections, one section to be used for radiocarbon age , one for loss on ignition, and the remainder to be kept for future needs.

openOpenApr 2018View details →

Eight Mile Lake Research Watershed, Carbon in Permafrost Experimental Heating and Drying Research (DryPEHR): DryPEHR dates snow-free 2012-2017

This drying and warming experiment addresses the following questions: 1) Does ecosystem drying, warming and permafrost thaw cause a net release or uptake of C from the ecosystem to the atmosphere?, 2) Does the decomposition of old C that comprises the bulk of the soil C pool influence ecosystem C loss? 3) How do drying and warmign affect plant communities and ecosystem properties? We are answering these questions using a combined warming and drying experiment (DryPEHR), which is situated with the Carbon in Permafrost Experimental Heating Research (CiPEHR) project and located in an upland tundra field site near Healy, Alaska in the foothills of the Alaska Range. Warming treatment here refers to growing season air temperature warming (~1C) using open top chambers (OTC) combined with soil 'warming' using snow fences during the snow covered months. Drying is achieve using an automated pumping system that lowers the water table in the dry plots. Soil warming began in 2008; OTCs and drying in 2011. Date snow-free is recorded every spring; when each individual plot becomes completely snow-free.

openCC (other)Jan 2020View details →

PIE LTER location and sample dates for sites used in space for time sea level rise study, Rowley, MA.

This dataset contains the GPS-ed locations of the quadrats used for the 2017-2018 Space for Time substitution experiment in tidal creek marshes off the Rowley River and Plum Island Sound in Rowley Massachusetts. The space for time study uses an intensive and comprehensive approach to compare low elevation, Spartina alterniflora marsh areas to higher elevation Spartina patens marsh areas. Other related data files include: HTL-RO-ST-MAR-Biomass, HTL-RO-ST-MAR-Birds, HTL-RO-ST-MAR-Quads, HTL-RO-ST-MAR-Sediments, HTL-RO-ST-MAR-Bites, HTL-RO-ST-MAR-Sticky, HTL-RO-ST-MAR-Decomp, HTL-RO-ST-MAR-Traps, HTL-RO-ST-MAR-Deep_pitfalls

openCC (other)Jan 2020View details →

PIE LTER, Year 2017-2018, locations, date, sediment concentration and spectral reflectance measurement methods of 40 water samples at Plum Island Sound and deep ocean, Massachusetts.

PIE LTER, Year 2017-2018, locations, date, sediment concentration and spectral reflectance measurement methods of 40 water samples at Plum Island Sound and deep ocean, Massachusetts

opencc-zeroAug 2020View details →

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior onBayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effectof the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyze datasets containing both populations and species variation when its computational-efficiency is needed.

opencc-by-4.0Aug 2020View details →

U-Th dating of lake sediments: Lessons from the 700 ka sediment record of Lake Junín, Peru — Datasets

Title: U-Th dating of lake sediments: Lessons from the 700 ka sediment record of Lake Junín, Peru — Datasets Version: 2.0 Date of Release: August 18, 2020 Last Update: September 16, 2020 Identifier: 10.5281/zenodo.4031644 Permalink: <a href="https://doi.org/10.5281/zenodo.4031644">https://doi.org/10.5281/zenodo.4031644</a> Associated publication: Chen, C.Y., McGee, D., Woods, A., Pérez, L., Hatfield, R.G., Edwards, R.L., Cheng, H., Valero-Garcés, B.L., Lehmann, S.B., Stoner, J.S., Schwalb, A., Tal, I., Seltzer, G.O., Tapia, P.M., Abbott, M.B., and Rodbell, R.T. (2020) U-Th dating of lake sediments: Lessons from the 700 ka sediment record of Lake Junín, Peru. Quaternary Science Reviews. 244: 106422 doi: <a href="https://doi.org/10.1016/j.quascirev.2020.106422">10.1016/j.quascirev.2020.106422</a> Link to publication: <a href="http://doi.org/10.1016/j.quascirev.2020.106422">https://doi.org/10.1016/j.quascirev.2020.106422</a> Suggested citation: Please reference the associated publication above when using any datasets or materials in this repository. Contact information: Christine Y. Chen, cychen@caltech.edu OR cychen.earth@gmail.com Dates of data collection and generation: February 2016 to July 2019 --------------- VERSION NOTES (v2.0) This online data repository was updated in order to correct errors in the U-Th data tables (Tables A1, A2, and A3) and subsequently update the age-depth model. The corrections impacted the files named 'CYChen et al. (2020) QSR - U-Th Data Tables for PLJ-1 and 1996 cores - v2.xlsx' and 'CYChen et al. (2020) QSR - Input Your Own Depths for Age-Depth Model - v2.xlsx'. No changes have been made to the original versions of other datasets. However, all components of this data repository have been given the "v2" identifier to be consistent with the versioning scheme applied to this data repository as a whole by Zenodo. --------------- DESCRIPTION OF DATA This data repository contains the following datasets and supplementary materials. Specific documentation and, where applicable, instructions of use are included in the readme section of each file. We refer the user to the original manuscript (see above) and the text of the Supplemental Materials published alongside this manuscript for additional general information regarding the collection and generation of these data. SUPPLEMENTARY TEXT AND FIGURES <ul> <li>CYChen et al. (2020) QSR - Supplementary Materials.pdf</li> </ul> DATA TABLES FOR PLJ-1 and 1996 CORE <ul> <li>CYChen et al. (2020) QSR - U-Th Data Tables for PLJ-1 and 1996 cores - v2.xlsx:  U-Th data tables for the PLJ-1 and 1996 core (with all digits preserved where possible, for reproducibility and data longevity)</li> <li>CYChen et al. (2020) QSR - Other Data for PLJ-1 core - v2.xlsx: sample locations and corresponding elemental concentrations, carbon coulometry, and color reflectance data</li> <li>CYChen et al. (2020) QSR - Ostracode Analysis for PLJ-1 core - v2.xlsx: ostracode paleoecological data from the PLJ-1 core</li> </ul> MODELING URANIUM-THORIUM ISOTOPIC EVOLUTION OF LAKE SEDIMENTS <ul> <li>CYChen et al. (2020) QSR - Modeling Spreadsheet for Uranium-Thorium Isotopic Evolution of Lake Sediments - v2.xlsx: spreadsheet for simulating the uranium-thorium isotopic evolution of a sample that has undergone open system behavior with respect to uranium and/or a sample of mixed composition (an impure carbonate)</li> </ul> AGE-DEPTH MODEL <ul> <li>CYChen et al. (2020) QSR - Input Your Own Depths for Age-Depth Model - v2.xlsx: spreadsheet for extracting the radiometric-based age-depth model generated by Bacon by splice depth</li> </ul>

opencc-zeroOct 2020View details →

Treelists, constraints and logfiles for: Relative time constraints improve molecular dating

Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. This is the case for instance for horizontal gene transfer events and ancient coevolutionary relationships such as (endo)symbioses, which can imply temporal relationships between two nodes in a phylogeny (Davin et al. 2018). This can be particularly helpful when the geological record is sparse, e.g. for microorganisms, which represent the vast majority of extant and extinct biodiversity. Here, we demonstrate that relative age constraints, when combined with fossil calibrations, can significantly improve both the accuracy and resolution of molecular clock estimates. We provide an implementation of relative age constraints in RevBayes (Hoehna et al. 2016) that can be combined in a modular manner with the wide range of molecular dating methods available in the software. To validate our method in a realistic data setting we apply it to two data sets of 40 Cyanobacteria and 62 Archaea respectively, and provide cross-validations of fossil calibrations and relative age constraints.

opencc-by-4.0Oct 2020View details →

Dates and Places of Birth and Death in the Biographical Dictionary of Republican China

This dataset contains the data on birth and death of the 589 historical figures in the Biographical Dictionary of Republican China. The file includes several tabs. The main data is located in the "data" tab. All the other tabs provide statistical analysis of the different variables included in the Data tab.

opencc-byAug 2017View details →

KD040-002002 - Round Tower - Graffiti Date

A small stone on the Castledermot Round Tower has a date of 1657 inscribed. It may coincide with the period when the church was refurbished in the 17th century after being damaged by Cromwell's forces. Source Archaeology.ie - The lower portion of the round tower survives (H. c. 20m). It is of granite with limestone pinnings (int diam. 2.5m; wall Th 2.37m). There are five floors with medieval crenellations above two string courses, but the modern floors do not correspond to the original levels. The entrance is at ground level through a flat lintelled battered doorway. There is an arched window on the first floor, and a flat headed windows between the second and third floors. The windows at the top, and the crenelations are of sixteenth century date. It is joined to the church by a vaulted corridor with wicker centring, of fifteenth century type. Survey: [@Dh_Age](https://www.digitalheritageage.com/) Funded: Kildare County Council Community Heritage Grant 2017 Source: Objaverse 1.0 / Sketchfab

opencc-by-4.0Oct 2016View details →

Dataset 1: All homozygous mutant embryo phenotypes from lethal and sub-viable lines scored by DMDD to date (Nov 2016)

The table lists the annotation data from homozygous mutant embryos that is the basis of the study. For every annotation the gene symbol, MGI_ID, allele symbol, DMDD_ID, MP term, ID and name is listed. In some cases the same MP term is listed more than once for a specific embryo (DMDD_ID), indicating the phenotypic abnormality was observed more than once in that embryo.

opencc-by-4.0Feb 2017View details →

Dataset 2: All wild type embryo phenotypes from lethal and sub-viable lines scored by DMDD to date (Nov 2016)

The table lists the annotation data from wild type embryos that is the basis of the study. For every annotation the gene symbol, MGI_ID, allele symbol, DMDD_ID, MP term, ID and name is listed. In some cases the same MP term is listed more than once for a specific embryo (DMDD_ID), indicating the phenotypic abnormality was observed more than once in that embryo.

opencc-by-4.0Jun 2017View details →

Galaxy Training Date for "Analyses of metagenomic data - The global picture"

These training datasets are part of a Galaxy Training Network tutorial that analyzes metagenomic (amplicon and WGS) data. These datasets are extracted of a project studying the Argentinean agricultural pampean soils (https://www.ebi.ac.uk/metagenomics/projects/SRP016633).

opencc-zeroNov 2023View details →

EOU UK central heating on/off date micro-survey result

When do UK Twitter users (2017 to 2022) turn their central heating fully off, by month? This informal periodic survey on social media suggests that a substantial fraction of respondents (up to 10%) leave their central heating on year-round, which may lead to unnecessary energy consumption and carbon emissions.

opencc-by-4.0May 2023View details →

Fig. 3 in On the date of original description and the type locality of Zygaena ampellophaga (Lepidoptera: Zygaenidae: Procridinae)

Fig. 3. Illustrations of Sphinx ampelophaga [sic] (1822) in the publication of Hübner (1818–1822).

opencc-by-4.0May 2023View details →

Fig. 2 in On the date of original description and the type locality of Zygaena ampellophaga (Lepidoptera: Zygaenidae: Procridinae)

Fig. 2. Illustrations of Zygaena ampellophaga in the original description by Bayle-Barelle (1809b).

opencc-by-4.0Nov 2023View details →

Stable oxygen and hydrogen isotope values for permafrost ice, rain, and snow collected near Fairbanks, Alaska and a summary of all age dates from the CRREL Permafrost Tunnel

Stable oxygen and hydrogen isotope values for permafrost ice, rain, and snow collected near Fairbanks, Alaska as well as a summary of all age dates from the CRREL Permafrost TunnelPlease contact me for more information or to use the data.thomas.a.douglas@usace.army.mil

opencc-zeroNov 2023View details →

Data from: Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses

Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae", whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models, and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.