77 Works

Diverse arsenic-containing lipids in the surface ocean

Katherine Heal, Ashley Maloney, Anitra Ingalls & Randelle Bundy
Arsenic is present at nanomolar levels throughout the ocean, and microbes assimilate this potentially toxic element due to its similarity to inorganic phosphorus. Although dissolved arsenic has been a focus of several oceanographic studies, the size and chemical character of the particulate arsenic pool is poorly understood. We measured particulate arsenic in five samples from the open ocean and determined the contribution of arsenic-containing lipids to this pool. Here we show that the accumulation of...

Optimal test-assisted quarantine strategies for COVID-19

Bo Peng, Wen Zhou, Rowland Pettit, Patrick Yu, Peter Matos, Alexander Greninger, Julie McCashin & Christopher Amos
Objective: To evaluate the effectiveness of SARS-CoV-2 testing on shortening the duration of quarantines for COVID-19 and to identify the most effective choices of testing schedules. Design: We performed extensive simulations to evaluate the performance of quarantine strategies when one or more SARS-CoV-2 tests were administered during the quarantine. Simulations were based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available testing methods. Sensitivity analyses were performed...

Forecasts, neural networks, and results from the paper: 'Seasonal Arctic sea ice forecasting with probabilistic deep learning'

Tom R. Andersson & J. Scott Hosking
This dataset encompasses data produced in the study 'Seasonal Arctic sea ice forecasting with probabilistic deep learning', published in Nature Communications. The study introduces a new Arctic sea ice forecasting AI system, IceNet, which predicts monthly-averaged sea ice probability (SIP; probability of sea ice concentration > 15%) up to 6 months ahead at 25 km resolution. The study demonstrated IceNet's superior seasonal forecasting skill over a state-of-the-art physics-based sea ice forecasting system, ECMWF SEAS5, and...

Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)

Timothy O'Connor, Marissa Sandoval, Jiarui Wang, Jacob Hans, Risa Takenaka, & Noah Whiteman
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across...

Chemical effects of snowmelt on an alpine lake in the Wind River Range, WY

Taylor Ganz & Gaboury Benoit
Nitrogen deposition from air pollution is increasingly reaching alpine lakes where the addition of nitrate and ammonium to sensitive surface waters can cause acidification and or eutrophication. Thirty years of sampling in the Wind River Range, WY have shown some lakes increasing in nitrogen. We sought to determine (1) if nutrient concentrations in Deep Lake increase during snowmelt when atmospheric deposition is released from the snowpack and (2) assess if the sampling season, location, meteorological...

Data from: Early origin of sweet perception in the songbird radiation

Yasuka Toda, Meng-Ching Ko, Qiaoyi Liang, Eliot Miller, Alejandro Rico-Guevara, Tomoya Nakagita, Ayano Sakakibara, Kana Uemura, Timothy Sackton, Takashi Hayakawa, Simon Yung Wa Sin, Yoshiro Ishimaru, Takumi Misaka, Pablo Oteiza, James Crall, Scott Edwards, Shuichi Matsumura & Maude Baldwin
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large radiation containing nearly half of all living birds. We demonstrate...

The dark side of rocks: an underestimated high-quality food resource in river ecosystems

Fen Guo, Stuart Bunn, Michael Brett, Hannes Hager & Martin Kainz
This dataset contains data of fatty acid profiles described in the paper: “Guo et al. (2021) The dark side of rocks: an underestimated high-quality food resource in river ecosystems. Journal of Ecology, https://doi.org/10.1111/1365-2745.13647”. This study was a field investigation conducted along a subalpine river continuum in Austria and aimed to identify the nutritional role of a “hidden” food resource for aquatic consumers; the biofilms growing on the underside of rocks (dark biofilms). Dark and light...

Data for: Radiative feedbacks on land surface change and associated tropical precipitation shifts

Marysa Lague, William Boos & Abigail Swann
Changes in land surface albedo and land surface evaporation modulate the atmospheric energy budget by changing temperatures, water vapor, clouds, snow and ice cover, and the partitioning of surface energy fluxes. Here idealized perturbations to land surface properties are imposed in a global model to understand how such forcings drive shifts in zonal mean atmospheric energy transport and zonal mean tropical precipitation. For a uniform decrease in global land albedo, the albedo forcing and a...

Evolutionary implications of dental anomalies in bats

Diego A Esquivel, Renan Maestri & Sharlene E Santana
The gain or loss of anatomical features is an important mechanism of morphological evolution and ecological adaptation. Dental anomalies –the loss or gain of teeth– are widespread and a potential source of craniodental specialization among mammals, yet their macroevolutionary patterns have been rarely explored. We present the first phylogenetic comparative study of dental anomalies across the second largest mammal Order, Chiroptera (bats). We conducted an extensive literature review and surveyed a large sample of museum...

Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards

Damien Esquerre, Scott Keogh, Diego Demangel, Mariana Morando, Luciano Avila, Francisco Ferri-Yáñez & Adam Leaché
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study,...

Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE

Thanaphong Phongpreecha, Chandresh Gajera, Candace Liu, Kausalia Vijayaragavan, Alan Chang, Martin Becker, Ramin Fallahzadeh, Rosemary Fernandez, Nadia Postupna, Emily Sherfield, Dmitry Tebaykin, Caitlin Latimer, Carol Shively, Thomas Register, Suzanne Craft, Kathleen Montine, Edward Fox, Kathleen Poston, C. Dirk Keene, Michael Angelo, Sean Bendall, Nima Aghaeepour & Thomas Montine
Synaptic molecular characterization is limited for Alzheimer’s disease (AD). Our newly invented mass cytometry-based method, Synaptometry by Time of Flight (SynTOF), was used to measure 38 antibody probes in approximately 17 million single-synapse events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), non-human primates (NHP), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice...

UCE alignments and phylogenetic trees

Christopher Blair, Robert Bryson, Uri Garcia-Vazquez, Adrian Nieto-Montes De Oca, David Lazcano, John McCormack & John Klicka
Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a timeframe for biological diversification across the Mexican Transition...

Interactions with soil fungi alter density-dependence and neighborhood effects in a locally abundant dipterocarp species

Kabir Peay, Richard Segnitz & Sabrina Russo
Seedling recruitment can be strongly affected by the composition of nearby plant species. At the neighborhood scale (on the order of tens of meters), adult conspecifics can modify soil chemistry and presence of host microbes (pathogens and mutualists) across their combined canopy area or rooting zones. At local or small spatial scales (on the order of one to few meters), conspecific seed or seedling density can influence the strength of intraspecific light and resource competition...

Efficient light‐harvesting of mesophotic corals is facilitated by coral optical traits

Netanel Kramer, Raz Tamir, Or Ben Zvi, Steven Jacques, Yossi Loya & Daniel Wangpraseurt
Sustained light-dependent coral reef communities can be found at a wide range of light environments, extending from the sea level to as deep as 150 m (i.e., mesophotic). How mesophotic corals thrive despite extremely limited light conditions still requires further investigation. Here, we undertook a comprehensive ecophysiological and bio-optical study on four depth-generalist coral species aiming to delineate the functional role that optical trait-properties have in light-harvesting, at contrasting light regimes. We show that the...

Multiple-model stock assessment frameworks for precautionary management and conservation on fishery-targeted coastal dolphin populations off Japan

Yu Kanaji, Hikari Maeda, Hiroshi Okamura, Andre Punt & Trevor Branch
1. Stock assessment approaches are often oversimplified due to lack of biological knowledge and insufficient data. In spite of worldwide attention, fishery-targeted coastal dolphin species in Japan have lacked in-depth quantitative stock assessments because of limited time-series of population size and an absence of associated biological information. We consequently developed integrated population models that analyzed multiple sources of data simultaneously with published biological information within a Bayesian framework. 2. We estimate population status and trends...

Data from: Walrus teeth as biomonitors of trace elements in Arctic marine ecosystems

Casey Clark, Lara Horstmann & Nicole Misarti
Effective biomonitoring requires an understanding of the factors driving concentrations of the substances or compounds of interest in the tissues of studied organisms. Biomonitoring of trace elements, and heavy metals in particular, has been the focus of much research; however, the complex roles many trace elements play in animal and plant tissues can make it difficult to disentangle environmental signals from physiology. This study examined the concentrations of 15 trace elements in the teeth of...

Grasshopper species’ seasonal timing underlies shifts in community phenological overlap in response to climate gradients, variability, and change

César Nufio, Stuart Graham & Lauren Buckley
1. Species with different life histories and communities that vary in their seasonal constraints tend to shift their phenology (seasonal timing) differentially in response to climate warming. 2. We investigate how these variable phenological shifts aggregate to influence phenological overlap within communities. Phenological advancements of later-season species and extended durations of early-season species may increase phenological overlap, with implications for species’ interactions such as resource competition. 3. We leverage extensive historic (1958-1960) and recent (2006-2015)...

Data from: Mammal-bearing gastric pellets potentially attributable to Troodon formosus at the Cretaceous Egg Mountain locality, Two Medicine Formation, Montana, U.S.A.

William Freimuth, David Varricchio, Alexandria Brannick, Lucas Weaver & Gregory Wilson Mantilla
Fossil gastric pellets (regurgitalites) have distinct taphonomic characteristics that facilitate inferences of behavioural ecology in deep time, despite their rarity in the fossil record. Using the taphonomic patterns of both extant and fossil small mammals from more recent geologic deposits as a guide, we assess the taphonomy of three unusual multi-individual aggregates of mammal skeletons from paleosols at Egg Mountain, a dinosaur nesting locality from the Upper Cretaceous Two Medicine Formation, Montana, USA. One aggregate...

The moment of tooth: rate, fate, and pattern of Pacific lingcod dentition revealed by pulse-chase

Emily Carr, Adam Summers & Karly Cohen
Tooth replacement rates of polyphyodont cartilaginous and bony fishes are hard to determine because of lack of obvious patterning, and maintaining specimens long enough to observe replacement. Pulse-chase is a fluorescent technique that differentially colours developing mineralized tissue. We present in-situ tooth replacement rate and position data for the oral and pharyngeal detentions of Ophiodon elongatus (Pacific lingcod). We assessed over 10,000 teeth, in 20 fish, and found a daily replacement rate of about two...

New and modified scores in the phylogenetic matrix from Schoch (2013)

Bryan Gee
Temnospondyl amphibians are a common component of non-marine Triassic assemblages, including in the Fremouw Formation (Lower to Middle Triassic) of Antarctica. Temnospondyls were among the first tetrapods to be collected from Antarctica, but their record from the lower Fremouw Formation has long been tenuous. One taxon, ‘Austrobrachyops jenseni,’ is represented by a type specimen comprising only a partial pterygoid, which is now thought to belong to a dicynodont. A second taxon, ‘Cryobatrachus kitchingi,’ is represented...

Fly and mouse tracking models and kinematics related to Anipose toolkit paper

Pierre Karashchuk, Sarah Walling-Bell, Elischa Sanders, Eiman Azim, Katie L. Rupp, Evyn S. Dickinson, Bingni W. Brunton & John C. Tuthill
This is a series of datasets related to the Anipose paper. We provide these to allow others to reproduce our tracking results and build upon them. Anipose is an open-source toolkit for robust markerless 3D pose estimation. Anipose is built on the 2D tracking method DeepLabCut, so users can expand their existing experimental setups to obtain accurate 3D tracking. It consists of four components: (1) a 3D calibration module, (2) filters to resolve 2D tracking...

Enabling conditions for an equitable and sustainable blue economy

Andrés M. Cisneros-Montemayor, Marcia Moreno-Baez, Gabriel Reygondeau, William W.L. Cheung, Katherine M. Crosman, Pedro C. Gonzalez-Espinosa, Vicky W.Y. Lam, Muhammed A. Oyinlola, Gerald G. Singh, Wilf Swartz, Yoshitaka Ota & Chong-Wei Zheng
The future of the global ocean economy is currently envisioned as an advancement towards a ‘Blue Economy’—socially equitable, environmentally sustainable, and economically viable ocean industries. However, there are current tensions between development discourses from perspectives of natural capital versus social equity and environmental justice. Here we show there are stark differences in Blue Economy outlooks when social conditions and governance capacity beyond resource availability are considered, and highlight limits to establishing multiple overlapping industries. The...

Stable isotopes reveal variation in consumption of Pacific salmon by brown bears, despite ready access in small streams

Aaron Wirsing, Hyejoo Ro, Jennifer H. Stern, Aaron J. Wirsing & Thomas P. Quinn
Brown bears Ursus arctos consume a wide range of organisms, including ungulates and plants, but Pacific salmon Oncorhynchus spp. are especially important to their diet where their ranges overlap. Although some brown bears minimize antagonistic encounters with other brown bears or infanticide by avoiding streams where salmon spawn, studies generally assume that brown bears with ready access to salmon feed heavily on them. To test this assumption, and the hypothesis that male brown bears would...

Data from: Evidence for ephemeral ring species formation during the diversification history of Western Fence Lizards (Sceloporus occidentalis)

Nassima Bouzid, James Archie, Roger Anderson, Jared Grummer & Adam Leaché
Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographic structure and evolutionary history of population divergence within Sceloporus occidentalis (Western Fence Lizards), a habitat generalist with a broad distribution that spans the major biogeographic regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny, and demography. Population...

7-Dehydrocholesterol-derived oxysterols cause neurogenic defects in Smith-Lemli-Opitz syndrome

Libin Xu, Hideaki Tomita & Josi Herron
Defective 3beta-hydroxysterol-delta7 -reductase (DHCR7) in the developmental disorder, Smith-Lemli-Opitz syndrome (SLOS), results in deficiency in cholesterol and accumulation of its precursor, 7-dehydrocholesterol (7-DHC). Here, we show that loss of DHCR7 causes accumulation of 7-DHC-derived oxysterol metabolites, premature neurogenesis, and perturbation of neuronal localization in developing murine or human cortical neural precursors, both in vitro and in vivo. We found that a major oxysterol, 3b,5a-dihydroxycholest-7-en-6-one (DHCEO), mediates these effects by initiating crosstalk between glucocorticoid receptor (GR)...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Washington
  • University of Cambridge
  • Stanford University
  • University of California, Berkeley
  • University of California, Santa Barbara
  • University of British Columbia
  • The Nature Conservancy
  • University of Glasgow
  • University of California, San Diego
  • The University of Texas at Arlington