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2. Data for: "The origin of non-skeletal carbonate mud and implications for global climate"

Author(s):
Geyman, Emily C.; Wu, Ziman; Nadeau, Matthew D.; Edmonsond, Stacey; Turner, Andrew; Purkis, Sam J.; Howes, Bolton; Dyer, Blake; Ahm, Anne-Sofie C.; Yao, Nan; Deutsch, Curtis A.; Higgins, John A.; Stolper, Daniel A.; Maloof, Adam C.
Abstract:
Carbonate mud represents one of the most important geochemical archives for reconstructing ancient climatic, environmental, and evolutionary change from the rock record. Mud also represents a major sink in the global carbon cycle. Yet, there remains no consensus about how and where carbonate mud is formed. In this contribution, we present new geochemical data that bear on this problem, including stable isotope and minor and trace element data from carbonate sources in the modern Bahamas such as ooids, corals, foraminifera, and green algae.
Type:
Dataset
Issue Date:
16 June 2022

3. Data set for "NAPS: Integrating pose estimation and tag-based tracking"

Author(s):
Wolf, Scott W.
Abstract:
Data set corresponding to "NAPS: Integrating pose estimation and tag-based tracking." This dataset contains the corresponding videos, tracking scripts, and SLEAP models along with SLEAP, NAPS, and ArUco tracking results.
Type:
Dataset
Issue Date:
7 December 2022

4. Three dimensional archaeocyathide and coral imagery for morphologic analysis

Author(s):
Manzuk, Ryan; Maloof, Adam
Abstract:
In our study, we compare the three dimensional (3D) morphologic characteristics of Earth's first reef-building animals (archaeocyath sponges) with those of modern, photosynthetic corals. Within this repository are the 3D image data products for both groups of animals. The archaeocyath images were produced through serial grinding and imaging with the Grinding, Imaging, and Reconstruction Instrument at Princeton University. The images in this repository are the downsampled data products used in our study, and the full resolution (>2TB) image stacks are available upon request from the author. For the coral image data, the computed tomography (CT) images of all samples are included at full resolution. Also included in this repository are the manual and automated outline coordinates of the archaeocyath and coral branches, which can be directly used for morphological study.
Type:
Dataset, Image, MovingImage, and StillImage
Issue Date:
August 2022

5. Code and data from "Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections"

Author(s):
King, Sean
Abstract:
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively. Included in this repository are the instructions and corresponding code required to build the dataset and run the analysis in the manuscript.
Type:
Dataset
Issue Date:
28 September 2021

7. Data for: 'Facies control on carbonate δ13C on the Great Bahama Bank'

Author(s):
Geyman, Emily C.; Maloof, Adam C.
Abstract:
The carbon isotopic (δ13C) composition of shallow-water carbonates often is interpreted to reflect the δ13C of the global ocean and is used as a proxy for changes in the global carbon cycle. However, local platform processes, in addition to meteoric and marine diagenesis, may decouple carbonate δ13C from that of the global ocean. To shed light on the extent to which changing sediment grain composition may produce δ13C shifts in the stratigraphic record, we present new δ13C measurements of benthic foraminifera, solitary corals, calcifying green algae, ooids, coated grains, and lime mud from the modern Great Bahama Bank (GBB). This survey of a modern carbonate environment reveals δ13C variability comparable to the largest δ13C excursions in the last two billion years of Earth history.
Type:
Dataset
Issue Date:
6 May 2021

8. Data for: 'How is sea level change encoded in carbonate stratigraphy?'

Author(s):
Geyman, Emily C.; Maloof, Adam C.; Dyer, Blake
Abstract:
The history of organismal evolution, seawater chemistry, and paleoclimate is recorded in layers of carbonate sedimentary rock. Meter-scale cyclic stacking patterns in these carbonates often are interpreted as representing sea level change. A reliable sedimentary proxy for eustasy would be profoundly useful for reconstructing paleoclimate, since sea level responds to changes in temperature and ice volume. However, the translation from water depth to carbonate layering has proven difficult, with recent surveys of modern shallow water platforms revealing little correlation between carbonate facies (i.e., grain size, sedimentary bed forms, ecology) and water depth. We train a convolutional neural network with satellite imagery and new field observations from a 3,000 km2 region northwest of Andros Island (Bahamas) to generate a facies map with 5 m resolution. Leveraging a newly-published bathymetry for the same region, we test the hypothesis that one can extract a signal of water depth change, not simply from individual facies, but from sequences of facies transitions analogous to vertically stacked carbonate strata. Our Hidden Markov Model (HMM) can distinguish relative sea level fall from random variability with ∼90% accuracy. Finally, since shallowing-upward patterns can result from local (autogenic) processes in addition to forced mechanisms such as eustasy, we search for statistical tools to diagnose the presence or absence of external forcings on relative sea level. With a new data-driven forward model that simulates how modern facies mosaics evolve to stack strata, we show how different sea level forcings generate characteristic patterns of cycle thicknesses in shallow carbonates, providing a new tool for quantitative reconstruction of ancient sea level conditions from the geologic record.
Type:
Dataset
Issue Date:
1 February 2021

9. Data for: Three-Dimensional Morphometry of Ooids in Oolites: a new tool for more accurate and precise paleoenvironmental interpretation

Author(s):
Howes, Bolton; Mehra, Akshay; Maloof, Adam
Abstract:
The prevalence of ooids in the stratigraphic record, and their association with shallow-water carbonate environments, make ooids an important paleoenvironmental indicator. Recent advances in the theoretical understanding of ooid morphology, along with empirical studies from Turks and Caicos, Great Salt Lake, and The Bahamas, have demonstrated that the morphology of ooids is indicative of depositional environment and hydraulic conditions. To apply this knowledge from modern environments to the stratigraphic record of Earth history, researchers measure the size and shape of lithified ooids on two-dimensional surfaces (i.e., thin sections or polished slabs), often assuming that random 2D slices intersect the nuclei and that the orientation of the ooids is known. Here we demonstrate that these assumptions rarely are true, resulting in errors of up to 35% on metrics like major axis length. We present a method for making 3D reconstructions by serial grinding and imaging, which enables accurate measurement of the morphology of individual ooids within an oolite, as well as the sorting and porosity of a sample. We also provide three case studies that use the morphology of ooids in oolites to extract environmental information. Each case study demonstrates that 2D measurements can be useful if the environmental signal is large relative to the error from 2D measurements. However, 3D measurements substantially improve the accuracy and precision of environmental interpretations. This study focuses on oolites, but errors from 2D measurements are not unique to oolites; this method can be used to extract accurate grain and porosity measurements from any lithified granular sample.
Type:
Dataset
Issue Date:
22 February 2021

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