80 Works

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...

Data from: Decoupling transcription factor expression and activity enables dimmer switch gene regulation

Chiara Ricci-Tam, Jue Wang, Ishay Ben-Zion, Julius Palme, Ang Li, Yonatan Savir & Michael Springer
Gene-regulatory networks achieve complex mappings of inputs to outputs through mechanisms that are poorly understood. We found that in the galactose-responsive pathway in Saccharomyces cerevisiae, the decision to activate the transcription of genes encoding pathway components is controlled independently from the expression level, resulting in behavior resembling that of a mechanical dimmer switch. This was not a direct result of chromatin regulation or combinatorial control at galactose-responsive promoters; rather, this behavior was achieved by hierarchical...

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...

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...

Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally

Carlos Alberto Arnillas, Elizabeth Borer, Eric Seabloom, Juan Alberti, Selene Baez, Jonathon Bakker, Elizabeth Boughton, Yvonne Buckley, Miguel Bugalho, Ian Donohue, John Dwyer, Jennifer Firn, Riley Gridzak, Nicole Hagenah, Yann Hautier, Aveliina Helm, Anke Jentsch, , Kimberly Komatsu, Lauri Laanisto, Ramesh Laungani, Rebecca McCulley, Joslin Moore, John Morgan, Pablo Peri … & Marc Cadotte
Biotic and abiotic factors interact with dominant plants —the locally most frequent or with the largest coverage— and non-dominant plants differently, partially because dominant plants modify the environment where non-dominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing non-dominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually...

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...

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...

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)...

Heroic Repair: Labor and Disaster

Megan Finn
The 1906 San Francisco Earthquake and Fire broke physical information and communication technologies at the very moment that people wanted to connect with loved ones using the telegraph – the quickest way to send messages. Sending telegrams was one means by which people connected with each other, but the telegraphic infrastructure, like much of the physical infrastructure, was badly damaged. Telegraph operators labored long hours to repair the telecommunications infrastructures or to enact workarounds. The...

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...

Benzalkonium Chloride Disinfectants Induce Apoptosis, Inhibit Proliferation, and Activate the Integrated Stress Response in a 3-D in Vitro Model of Neurodevelopment

Josi Herron, Libin Xu, Hideaki Tomita, Collin White & Terrance Kavanagh
We previously found that the widely used disinfectants, benzalkonium chlorides (BACs), alter cholesterol and lipid homeostasis in neuronal cell lines and in neonatal mouse brains. Here we investigate the effects of BACs on neurospheres, an in vitro three-dimensional model of neurodevelopment. Neurospheres cultured from mouse embryonic neural progenitor cells (NPCs) were exposed to increasing concentrations (1 to 100 nM) of a short-chain BAC (BAC C12), a long-chain BAC (BAC C16), and AY9944 (a known DHCR7...

Tactile active sensing in an insect-plant pollinator

Tanvi Deora, Mahad Ahmed, Thomas Daniel & Bingni Brunton
The interaction between insects and the flowers they pollinate has driven the evolutionary diversity of both insects and flowering plants, two groups with the most numerous species on Earth. Insects use vision and olfaction to localize host plants, but we know relatively little about how they find the tiny nectary opening in the flower, which can be well beyond their visual resolution. Especially when vision is limited, touch becomes crucial in successful insect–plant pollination interactions....

Appendix: Association between hemostatic profile and migraine: a Mendelian randomization analysis

Yanjun Guo, Pamela Rist, Maria Sabater-Lleal, Paul De Vries, Nicholas Smith, Paul Ridker, Tobias Kurth & Daniel Chasman
Objective: To assess support for a causal relationship between hemostatic measures and migraine susceptibility using genetic instrumental analysis. Methods: Two-sample Mendelian randomization (MR) instrumental leveraging available genome-wide association study (GWAS) summary statistics was applied to hemostatic measures as potential causal for migraine and its subtypes, migraine with aura (MA) and migraine without aura (MO). Twelve blood-based measures of hemostasis were examined, including plasma level or activity of eight hemostatic factors and two fibrinopeptides together with...

Data for: A size principle for recruitment of Drosophila leg motor neurons

Anthony Azevedo, Evyn Dickinson, Pralaksha Gurung, Lalanti Venkatasubramanian, Richard Mann & John Tuthill
To move the body, the brain must precisely coordinate patterns of activity among diverse populations of motor neurons. In many species, including vertebrates, the motor neurons innervating a given muscle fire in a specific order that is determined by a gradient of cellular size and electrical excitability. This hierarchy allows premotor circuits to recruit motor neurons of increasing force capacity in a task-dependent manner. However, it remains unclear whether such a size principle also applies...

The hidden influence of communities in collaborative funding of clinical science

Kishore Vasan & Jevin West
Every year the National Institutes of Health allocates $10.7 billion (one-third of its funds) for clinical science research while the pharmaceutical companies spend $52.9 billion (90% of its annual budget). However, we know little about funder collaborations and the impact of collaboratively funded projects. As an initial effort towards this, we examine the cofunding network, where a funder represents a node and an edge signifies collaboration. Our core data include all papers that cite and...

Ten year camera trap dataset of tigers in India

Beth Gardner, Rahel Sollmann, N. Samba Kumar, Devcharan Jathanna & K. Ullas Karanth
1. With continued global changes, such as climate change, biodiversity loss and habitat fragmentation, the need for assessment of long-term population dynamics and population monitoring of threatened species is growing. One powerful way to estimate population size and dynamics is through capture-recapture methods. Spatial capture (SCR) models for open populations make efficient use of capture-recapture data, while being robust to design changes. Relatively few studies have implemented open SCR models and to date, very few...

Detection histories of mesocarnivores in agricultural areas of Southern Chile

Nicolás Gálvez, José Infante, Adrián Fernandez, Jesús Díaz & Lisanne Petracca
We obtained mesocarnivore detection/non-detection data from 180 sampling units (4 km2 each) located in the agricultural landscapes of southern Chile from January-April of 2019. We used single-species occupancy models to investigate the associations of forest fragmentation, forest loss, and private land ownership subdivision (as a measure of human use intensification) with the occurrence of four mesocarnivores (güiña, grey fox, culpeo fox, and Molina’s hog-nosed skunk), and extended this framework to two-species occupancy models to assess...

Variation in the modality of a yeast signaling pathway is mediated by a single regulator

Julius Palme, Jue Wang & Michael Springer
Bimodal gene expression by genetically identical cells is a pervasive feature of signaling networks, and has been suggested to allow organisms to hedge their "bets" in uncertain conditions. In the galactose-utilization (GAL) pathway of Saccharomyces cerevisiae, gene induction is unimodal or bimodal depending on natural genetic variation and pre-induction conditions. Here, we find that this variation in modality arises from regulation of two features of the pathway response: the fraction of cells that show induction,...

Data from: Examining the dynamics of Epstein-Barr virus shedding in the tonsils and the impact of HIV-1 coinfection on daily saliva viral loads

Catherine Byrne, Christine Johnston, Jackson Orem, Fred Okuku, Meei-Li Huang, Habibur Rahman, Anna Wald, Lawrence Corey, Joshua Schiffer, Corey Casper, Daniel Coombs & Soren Gantt
Epstein-Barr virus (EBV) is transmitted by saliva and is a major cause of cancer, particularly in people living with HIV/AIDS. Here, we describe the frequency and quantity of EBV detection in the saliva of Ugandan adults with and without HIV-1 infection and use these data to develop a novel mathematical model of EBV infection in the tonsils. Eligible cohort participants were not taking antiviral medications, and those with HIV-1 infection had a CD4 count >200...

Cryptic diversity across the Trans-Mexican Volcanic Belt of Mexico in the montane bunchgrass lizard Sceloporus subniger (Squamata: Phrynosomatidae)

Robert Bryson, Jared Grummer, Elizabeth Connors, Joseph Tirpak, John McCormack & John Klicka
Sceloporus subniger Poglaygen & Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting S. subniger may be a composite of several distinct species, we examined in more detail the genetic structure of S. subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing...

Data from: Incomplete convergence of gliding-mammal skeletons

David Grossnickle
Ecology and biomechanics play central roles in the generation of phenotypic diversity. When unrelated taxa invade a similar ecological niche, biomechanical demands can drive convergent morphological transformations. Thus, identifying and examining convergence helps to elucidate the key catalysts of phenotypic change. Gliding mammals are often presented as a classic case of convergent evolution because they independently evolved in numerous clades, each possessing patagia (‘wing’ membranes) that generate lift during gliding. We use phylogenetic comparative methods...

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe & Tereza Jezkova
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here we explore...

Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)

Adam Leache, Hayden Davis, Sonal Singhal, Matt Fujita & Megan Lahti
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should...

Seasonality in Kgalagadi lizards: inferences from legacy data

Raymond Huey
This data set compiles field and dietary data on Kagalagadi lizards, collected in 1969-70. The data are used in: Huey, R. B., D. B. Miles, and E. R. Pianka. 2021. Seasonality in Kgalagadi lizards: Inferences from llegacy data. American Natualist in press. This paper addresses whether legacy data -- or other data that had been gathered for unrelated purposes -- can be relevant to contemporary ecological issues. The data used here were gathered a half-century...

Registration Year

  • 2021

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  • Journal Article
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  • University of Washington
  • Stanford University
  • University of Cambridge
  • 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