61 Works

The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections

Alisa Vershinina, Joshua D. Kapp, Gennady Baryshnikov & Beth Shapiro
Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here we analyze an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified...

Single-chain heteropolymers transport protons selectively and rapidly

Tao Jiang, Aaron Hall, Marco Eres, Zahra Hemmatian, Baofu Qiao, Yun Zhou, Zhiyuan Ruan, Andrew D. Couse, William T. Heller, Haiyan Huang, Monica Olvera De La Cruz, Marco Rolandi & Ting Xu
Precise protein sequencing and folding are believed to generate the natural channel structure and chemical diversity of proteins, both of which are essential to synthetically achieve proton transport performance comparable to that seen in natural systems. Geometrically defined channels have been fabricated using peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic frameworks; however, none of these channels rivals the performance observed in their natural counterparts. Here we show that without forming an atomically structured channel,...

How climate impacts the composition of wolf killed-elk in northern Yellowstone National Park

Christopher Wilmers, Matthew Metz, Daniel Stahler, Michel Kohl, Chris Geremia & Douglas Smith
1. While the functional response of predators is commonly measured, recent work has revealed that the age and sex composition of prey killed is often a better predictor of prey population dynamics because the reproductive value of adult females is usually higher than that of males or juveniles. 2. Climate is often an important mediating factor in determining the composition of predator kills, but we currently lack a mechanistic understanding of how the multiple facets...

Thermal pressure in the laser heated diamond anvil cell: a quantitative study and implications for the density vs. mineralogy correlation of the mantle

Ethan Yen, Quentin Williams & Martin Kunz
Thermal pressure is an inevitable thermodynamic consequence of heating a volumetrically constrained sample in the diamond anvil cell. Its possible influences on experimentally determined density-mineralogy correlations are widely appreciated, yet the effect itself has never been experimentally measured. We present here the first quantitative measurements of the spatial distribution of thermal pressure in a laser heated diamond anvil cell (LHDAC) in both olivine and AgI. The observed thermal pressure is strongly localized and closely follows...

Phylogenomic data reveal widespred introgression across the range of an alpine and arctic specialist

Erik Funk, Garth Spellman, Kevin Winker, Jack Withrow, Erika Zavaleta, Kristen Ruegg & Scott Taylor
Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects...

Ancient hybridization with an unknown population facilitated high altitude adaptation of canids

Ming-Shan Wang & Dong-Dong Wu Wu
Genetic introgression provides material for adaptive evolution, but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we use newly sequenced genomes of high-altitude Tibetan and Himalayan wolves to explore the evolutionary history and adaptation of this group. We find that Tibetan and Himalayan wolves are closely related to each other, and...

Inference of nonlinear receptive field subunits with spike-triggered clustering

Nishal Shah, Nora Brackbill, Colleen Rhoades, Alexandra Kling, Georges Goetz, Alan Litke, Alexander Sher, Eero Simoncelli & E.J. Chichilnisky
Responses of sensory neurons are often modeled using a weighted combination of rectified linear subunits. Since these subunits often cannot be measured directly, a flexible method is needed to infer their properties from the responses of downstream neurons. We present a method for maximum likelihood estimation of subunits by soft-clustering spike-triggered stimuli, and demonstrate its effectiveness in visual neurons. Subunits estimated from parasol retinal ganglion cells (RGCs) in macaque retina partitioned the receptive field into...

Field courses narrow demographic achievement gaps in ecology and evolutionary biology

Roxanne Beltran, Erin Marnocha, Alexandra Race, Don Croll, Gage Dayton & Erika Zavaleta
Disparities remain in the representation of marginalized students in STEM. Classroom-based experiential learning opportunities can increase student confidence and academic success; however, the effectiveness of extending learning to outdoor settings is unknown. Our objectives were to examine 1) demographic gaps in ecology and evolutionary biology (EEB) major completion, college graduation, and GPAs for students who did and did not enroll in field courses, 2) whether under-represented demographic groups were less likely to enroll in field...

Rapid adaptive evolution of the diapause program during range expansion of an invasive mosquito

Zachary A. Batz, Anthony J. Clemento, Jens Fitzenwanker, Timothy J. Ring, John Carlos Garza & Peter A. Armbruster
In temperate climates, the recurring seasonal exigencies of winter represent a fundamental physiological challenge for a wide range of organisms. In response, many temperate insects enter diapause, an alternative developmental program, including developmental arrest, that allows organisms to synchronize their life cycle with seasonal environmental variation. Geographic variation in diapause phenology contributing to local climatic adaptation is well documented. However, few studies have examined how the rapid evolution of a suite of traits expressed across...

Natural enemy-herbivore networks along local management and landscape gradients in urban agroecosystems

Stacy Philpott, Azucena Lucatero, Peter Bichier, Monika Egerer, Shalene Jha, Brenda Lin & Heidi Liere
Ecological networks can provide insight into how biodiversity loss and changes in species interactions impact the delivery of ecosystem services. In agroecosystems that vary in management practices, quantifying changes in ecological network structure across gradients of local and landscape composition can inform both the ecology and function of productive agroecosystems. In this study, we examined natural enemy-herbivore co-occurrence networks associated with Brassica oleracea (cole crops), a common crop in urban agricultural systems. Specifically, we investigated...

Año Nuevo Island Animal Count: analyzing citizen science pinniped counts from drone imagery

Sarah Wood
Fluctuations in marine mammal abundance can reveal changes in local ecosystem health and inform conservation strategies. Unmanned aircraft systems (UAS) such as drones are increasingly being used to photograph and count marine mammals in remote locations; however, counting animals in images is a laborious task. Crowd-sourced science has the potential to considerably reduce the time required to conduct these censuses but must first be validated against expert counts to confirm accuracy. Our objectives were to...

Gibbon genome (Nleu3.0) custom gene annotation file

Mariam Okhovat, Kimberly A. Nevonen, Brett A. Davis, Pryce Michener, Samantha Ward, Mark Milhaven, Lana Harshman, Ajuni Sohota, Jason D. Fernandes, Sofie R. Salama, Rachel J. O'Neill, Nadav Ahituv, Krishna R. Veeramah & Lucia Carbone
Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA, which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of...

Isotopic evidence for long-distance connections of the AD thirteenth century Promontory caves occupants

Jessica Metcalfe, John Ives, Sabrina Shirazi, Kevin Gilmore, Jennifer Hallson, Fiona Brock, Bonnie Clark & Beth Shapiro
The Promontory caves (Utah) and Franktown Cave (Colorado) contain high-fidelity records of short-term occupations by groups with material culture connections to the Subarctic/Northern Plains. This research uses Promontory and Franktown bison dung, hair, hide, and bone collagen to establish local baseline carbon isotopic variability and identify leather from a distant source. The ankle wrap of one Promontory Cave 1 moccasin had a δ13C value that indicates a substantial C4 component to the animal’s diet, unlike...

Physical and biogeochemical drivers of alongshore pH and oxygen variability in the California Current System

Jerome Fiechter & Julia Cheresh
In the California Current System (CCS), the nearshore environment experiences natural exposure to low pH and reduced oxygen in response to coastal upwelling. Anthropogenic impacts further decrease pH and oxygen below biological thresholds, making the CCS particularly vulnerable to ocean acidification and hypoxia. Results from a coupled physical-biogeochemical model reveal a strongly heterogeneous alongshore pattern of nearshore pH and oxygen in the central CCS, both in their long-term means and trends. This spatial structuring is...

Pluto and Charon limb profile topography

Jack Conrad
We derived updated and expanded topography datasets for Pluto and Charon. This is done through finding the body edge (i.e. the limb) in images, and with those body edge locations we can apply simple geographical techniques to produce limb profiles. The process involves some human intervention, but is primarily automation based. Our limb profile topography is useful for geologic and geophysical studies of Pluto and Charon. Additionally, we provide processed data of how we used...

UVS Occultation Altimetry Code and Synthetic Data

Jacob Abrahams
This contains the code used to produce the figures in our UVS Occultation Altimetry manuscript, as well as the observation locations and synthetic data required to run the code. There are 9 .txt files, one is our nominal shape model, one is the set of chord ingress and egress points, three of them contain the locations of radar altimetric measurements for different truncation altitudes, and four of them contain precomputed lengths corresponding to our nominal...

Lunar rhythms in growth of larval fish

Jeffrey S. Shima, Craig W. Osenberg, Erik G. Noonburg, Suzanne H. Alonzo & Stephen E. Swearer
Growth and survival of larval fishes is highly variable and unpredictable. Our limited understanding of this variation constrains our ability to forecast population dynamics and effectively manage fisheries. Here we show that daily growth rates of a coral reef fish (the sixbar wrasse, Thalassoma hardwicke) are strongly lunar-periodic and predicted by the timing of nocturnal brightness: growth was maximized when the first half of the night was dark and the second half of the night...

Diurnal timing of nonmigratory movement by birds: the importance of foraging spatial scales

Julie Mallon, Marlee Tucker, Annalea Beard, , Keith Bildstein, Katrin Böhning-Gaese, John Brzorad, Evan Buechley, Javier Bustamante, Carlos Carrapato, José Castillo-Guerrero, Elizabeth Clingham, Mark Desholm, Christopher DeSorbo, Robert Domenech, Hayley Douglas, Olivier Duriez, Peter Enggist, Nina Farwig, Wolfgang Fiedler, Anna Gagliardo, Clara García-Ripollés, Juan Antonio Gil, Morgan Gilmour, Roi Harel … & Bill Fagan
Timing of activity can reveal an organism’s efforts to optimize foraging either by minimizing energy loss through passive movement or by maximizing energetic gain through foraging. Here, we assess whether signals of either of these strategies are detectable in the timing of activity of daily, local movements by birds. We compare the similarities of timing of movement activity among species using six temporal variables: start of activity relative to sunrise, end of activity relative to...

Affect and Activism

Deborah Gould, Rory Barron, Brittany Frodge & Robby Hardesty
Deborah Gould is an Associate Professor of Sociology at the University of California, Santa Cruz (and Affiliated Faculty in Feminist Studies, History of Consciousness, and Politics). Her book Moving Politics: Emotion and ACT UP's Fight Against AIDS (University of Chicago Press, 2009) won the Distinguished Contribution to Scholarship Best Book Award from the American Sociological Association's Political Sociology Section (2010) and the Ruth Benedict Book Prize from the American Anthropological Association (2010). She is currently...

Distribution, Biomass, and Demography of Coastal Pelagic Fishes in the California Current Ecosystem During Summer 2019 Based on Acoustic-Trawl Sampling

Kevin L. Stierhoff, Juan P. Zwolinski & David A. (David Arthur) Demer
NOAA technical memorandum NMFS NOAA-TM-NMFS-SWFSC ; 626

Relaxed predation selection on rare morphs of Ensatina salamanders (Caudata: Plethodontidae) promotes a polymorphic population in a novel dune sand habitat

Sean Reilly, Caitlyn Rich & Barry Sinervo
The Ensatina ring species represents a classic example of locally adapted lineages. The Monterey Ensatina (Ensatina eschscholtzii eschscholtzii) is a cryptic subspecies with brown coloration, however, a recently discovered polymorphic population within a wind-blown sand region also contains leucistic (pink) and xanthistic (orange) morphs. Leucism/xanthism frequency was mapped across the subspecies’ range revealing that these morphs are generally rare or absent except within regions containing light-colored substrate. Attack rates were estimated using clay models of...

How to learn to recognize conspecific brood parasitic offspring

Daizaburo Shizuka & Bruce Lyon
Recognition systems evolve to reduce the risk and costs of making recognition errors. Two sources of recognition error include perceptual error (error arising from inability to discriminate between objects) and template error (error arising from using the wrong recognition template). We focus on how template error shapes host defense against avian brood parasites. Prior experiments in American coots (Fulica americana), a conspecific brood parasite, demonstrated how hosts learn to recognize brood parasitic chicks by using...

Tree mycorrhizal type mediates the strength of negative density dependence in temperate forests

Feng Jiang, Kai Zhu, Marc Cadotte & Guangze Jin
1. Recent plant-soil feedback experiments suggest that arbuscular mycorrhizal (AM) tree species experience stronger conspecific negative density dependence (CNDD) than ectomycorrhizal (EM) tree species. Yet how these findings inform our understanding of natural systems is limited because the roles of local soil conditions, light environments and tree species abundances in influencing CNDD for AM and EM species are not clear. 2. Here we examined seedling and sapling survival in two temperate old-growth forests (broadleaved pine...

Data from: Krill hotspot formation and phenology in the California Current Ecosystem

Jerome Fiechter
In the California Current Ecosystem (CCE), krill represent a key link between primary production and higher trophic level species owing to their central position in the food web and tendency to form dense aggregations. However, the strongly advective circulation associated with coastal upwelling may spatiotemporally decouple the occurrence and persistence of krill hotspots from phytoplankton biomass and nutrient sources. Results from a physical-biological model provide insights into fundamental mechanisms controlling the phenology of krill hotspots...

Data and code for: Microalgae-blend tilapia feed eliminates fishmeal and fish oil, improves growth, and is cost viable

Pallab Sarker, Anne Kapuscinski, Brandi McKuin, Devin Fitzgerald, Hannah Nash & Connor Greenwood
Aquafeed manufacturers have reduced, but not fully eliminated, fishmeal and fish oil and are seeking cost competitive replacements. We combined two commercially available microalgae, to produce a high-performing fish-free feed for Nile tilapia (Oreochromis niloticus) —the world’s second largest group of farmed fish. We substituted protein-rich defatted biomass of Nannochloropsis oculata (leftover after oil extraction for nutraceuticals) for fishmeal and whole cells of docosahexaenoic acid (DHA)-rich Schizochytrium sp. as substitute for fish oil. Here, we...

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text
  • Output Management Plan


  • University of California, Santa Cruz
  • Southwest Fisheries Science Center
  • University of California, Santa Barbara
  • Stanford University
  • University of California, Berkeley
  • California Polytechnic State University
  • California State University Los Angeles
  • Lawrence Berkeley National Laboratory
  • Seattle University
  • University of California, Davis