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Master spatial file for native California vascular plants used by Baldwin et al. (2017 Amer. J. Bot.)

Bruce G. Baldwin, Andrew H. Thornhill, William A. Freyman, David. D. Ackerly, Matthew M. Kling, Naia Morueta-Holme & Brent D. Mishler
Georeferenced locality information of all Californian native vascular plant species from herbarium specimens obtained from five different online sources in August 2015: (1) the Consortium of California Herbaria (CCH, http://ucjeps.berkeley.edu/consortium/), (2) the Consortium of Pacific Northwest Herbaria (http://www.pnwherbaria.org), (3) Australia’s Virtual Herbarium (avh.chah.org.au), (4) Canadensys (http://www.canadensys.net), and (5) the Global Biodiversity Information Facility (http://www.gbif.org). Data were carefully cleaned as described in Baldwin et al. 2017, and this final data set contains 1,383,762 occurrences.

Experimental and Supplementary Data for The Roles of Impact and Inertia in the Failure of a Shoelace Knot

Christopher Daily-Diamond, Christine Gregg & Oliver O'Reilly
Raw experimental data gathered during impulsive forcing of a shoelace knot on a pendulum apparatus, in various orientations, with corresponding data summary sheets. Also included are two supplementary video files of treadmill and pendulum tests.

Videos of Etching Gold Nanocubes and Nanorhombic Dodecahedra in Graphene Liquid Cell Transmission Electron Microscopy

Matthew Hauwiller, Justin Ondry & A. Paul Alivisatos
Liquid cell Transmission Electron Microscopy (TEM) provides the opportunity to view nanocrystal dynamics in their native liquid environment with the necessary spatial resolution. In this dataset, gold nanocubes and nano-rhombic dodecahedra are etched inside graphene liquid cells while viewing using TEM. The initial gold nanocrystals are synthesized and then loaded in water pockets sandwiched between sheets of graphene. These graphene pockets protect the liquid from the vacuum of the TEM column while not preventing the...

Habitat use, interspecific competition, and phylogenetic history shape the evolution of claw and toepad morphology in Lesser Antillean anoles

Michael Yuan, Catherine Jung, Marvalee Wake & Ian Wang
Ecologically functional traits are the product of several, at times opposing, selective forces. Thus, ecomorphological patterns can be disrupted locally by biotic interactions such as competition and may not be consistent across lineages. Here, we studied the evolution of claws and toepads in relation to macrohabitat (vegetation), use of structural microhabitat (perch height), and congeneric competition for two distantly-related Lesser Antillean anole clades: the bimaculatus and roquet series. We collect univariate and geometric morphometric data...

The interplay of climate, intervention and imported cases as determinants of the 2014 dengue outbreak in Guangzhou

Qu Cheng, Qinlong Jing, Robert C. Spear, John M. Marshall, Zhicong Yang & Peng Gong
Dengue is a fast spreading mosquito-borne disease that affects more than half of the population worldwide. An unprecedented outbreak happened in Guangzhou, China in 2014, which contributed 52 percent of all dengue cases that occurred in mainland China between 1990 and 2015. Our previous analysis, based on a deterministic model, concluded that the early timing of the first imported case that triggered local transmission and the excessive rainfall thereafter were the most important determinants of...

Slab Ocean forcing file and model output for \"Seasonal Transitions and the Westerly Jet in the Holocene East Asian Summer Monsoon\"

Wenwen Kong, Leif Swenson & John Chiang
This dataset contains slab ocean forcing file and key model outputs from CAM5 simulations used in: Kong, W., L.M. Swenson, and J.C.H. Chiang, Seasonal Transitions and the Westerly Jet in the Holocene East Asian Summer Monsoon. Journal of Climate, doi:10.1175/JCLI-D-16-0087.1 link

Chronic Arsenic Exposure Impairs Adaptive Thermogenesis in Male C57BL/6J Mice

Felicia Castriota
The global prevalence of type 2 diabetes (T2D) has doubled since 1980. Human epidemiological studies support arsenic exposure as a risk factor for T2D, although the precise mechanism is unclear. We hypothesized that chronic arsenic ingestion alters glucose homeostasis by impairing adaptive thermogenesis, i.e. body heat production in cold environments. Arsenic is a pervasive environmental contaminant, with more than 200 million people worldwide currently exposed to arsenic-contaminated drinking water. Male C57BL/6J mice exposed to sodium...

Wax Lake Delta Dataset

Hongxu Ma
The surrogate bio-volume and topography spatial dataset of Wax Lake Delta

Tributary confluences are dynamic thermal refuges for a juvenile salmonid in a warming river network

Terrance Wang, Suzanne Kelson, George Greer, Sally Thompson & Stephanie Carlson
As rivers warm, cold-water fish species may alleviate thermal stress by moving into localized thermal refuges such as cold-water plumes created by cool tributary inflows. We quantified use of two tributary confluence plumes by juvenile steelhead, Oncorhynchus mykiss, throughout the summer, including how trout positioned themselves in relation to temperature within confluence plumes. At two confluences, Cedar and Elder creeks, along the South Fork Eel River, California, USA, we monitored temperatures using in-situ logger grids...

Kinesin and dynein use distinct mechanisms to bypass obstacles

Luke S Ferro, Ahmet Yildiz, Sinan Can, Meghan A Turner & Mohamed M ElShenawy
Kinesin-1 and cytoplasmic dynein are microtubule (MT) motors that transport intracellular cargos. It remains unclear how these motors move along MTs densely coated with obstacles of various sizes in the cytoplasm. Here, we tested the ability of single and multiple motors to bypass synthetic obstacles on MTs in vitro. Contrary to previous reports, we found that mammalian dynein is highly capable of bypassing obstacles. Human kinesin-1 motors fail to avoid obstacles, consistent with their inability...

Data from: Allocation of gene products to daughter cells is determined by the age of the mother in single Escherichia coli cells

Ulla Rang, Chao Shi, Lin Chao, Audrey Proenca, Andrew Qiu & Jasper Chao
Gene expression and growth rate are highly stochastic in E. coli. Some of the growth rate variations result from the deterministic and asymmetric partitioning of damage by the mother to its daughters. One daughter, denoted the old daughter, receives more damage, grows more slowly, and ages. To determine if expressed gene products are also allocated asymmetrically, we compared the levels of expressed green fluorescence protein in growing daughters descending from the same mother. Our results...

Master spatial file for for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)

Andrew Thornhill, Bruce Baldwin, William Freyman, Sonia Nosratinia, Matthew Kling, Naia Morueta-Holme, Thomas Madsen, David Ackerly, Brent Mishler & Andrew Thornhill
Georeferenced locality information for 1083 OTUs assembled from all Californian native vascular plant records from herbarium specimens obtained from five different online sources in August 2015: (1) the Consortium of California Herbaria (CCH, http://ucjeps.berkeley.edu/consortium/), (2) the Consortium of Pacific Northwest Herbaria (http://www.pnwherbaria.org), (3) Australia’s Virtual Herbarium (avh.chah.org.au), (4) Canadensys (http://www.canadensys.net), and (5) the Global Biodiversity Information Facility (http://www.gbif.org). Data were carefully cleaned as described in Baldwin et al. 2017, and combined into OTUs as described...

Salmon Creek Organic Geochemistry Chemometric Data

Laurel Larsen, Laurel Larsen & Cleo Woelfle-Erskine
This datafile contains fluorescence indices and the results of a parallel factor analysis (PARAFAC) performed on samples collected within the Salmon Creek Watershed in Sonoma County, Califonia. Please see Woelfle-Erskine et al. (2017) for site location details. The present dataset is provided in support of Larsen and Woelfle-Erskine (in review). The purpose of this dataset was to develop a fluorescent fingerprint for purposes of differentiating between surface water, groundwater, and hyporheic water.

Salmon Creek radon data

Laurel Larsen & Cleo Woelfle-Erskine
This datafile contains results of 222Rn analysis of samples collected within the Salmon Creek Watershed in Sonoma County, Califonia. Please see Woelfle-Erskine et al. (2017) for site location details. The present dataset is provided in support of Larsen and Woelfle-Erskine (in review).The purpose of this dataset was to determine relative ages of water samples.Data were collected in 2016 in the Fay Creek and Tannery Creek watersheds, both second-order tributaries of Salmon Creek.For further information, please...

MHD Field line tracing results

Shaosui Xu
The zip file contains field line tracing results from a MHD simulation, which are used to create Figure 3 of manuscript #2017GL075831, titled as "High-altitude closed magnetic loops at Mars observed by MAVEN".

Data from: Subordinate plants mitigate drought effects on soil ecosystem processes by stimulating fungi

Pierre Mariotte, Bjorn J. M. Robroek, Vincent E. J. Jassey & Alexandre Buttler
The subordinate insurance hypothesis suggests that highly diverse communities contain greater numbers of subordinate species than less diverse communities. It has previously been reported that subordinate species can improve grassland productivity during drought, but the underlying mechanisms remain undetermined. Using a combination of subordinate species removal and summer drought, we show that soil processes play a critical role in community resistance to drought. Interestingly, subordinate species drive soil microbial community structure and largely mitigate the...

Data from: Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes

Anna M. Sturrock, J. D. Wikert, Timothy Heyne, Carl Mesick, Alan E. Hubbard, Travis M. Hinkelman, Peter K. Weber, George E. Whitman, Justin J. Glessner & Rachel C. Johnson
The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, and is thus central to many recovery efforts. However, in order to preserve and restore diversity in life history traits, it...

Data from: Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies

Bárbara Huber, Annabel Whibley, Yann Le Poul, Nicolas Navarro, Arnaud Martin, Simon Baxter, Abhijeet Shah, Benoît Gilles, Thierry Wirth, W. Owen McMillan & Mathieu Joron
Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have...

Data from: Diversification practices reduce organic to conventional yield gap

Lauren C. Ponisio, Leithen K. M'Gonigle, Kevi C. Mace, Jenny Palomino, Perry De Valpine, Claire Kremen, P. De Valpine, C. Kremen, L. K. M'Gonigle, K. C. Mace, J. Palomino & L. C. Ponisio
Agriculture today places great strains on biodiversity, soils, water and the atmosphere, and these strains will be exacerbated if current trends in population growth, meat and energy consumption, and food waste continue. Thus, farming systems that are both highly productive and minimize environmental harms are critically needed. How organic agriculture may contribute to world food production has been subject to vigorous debate over the past decade. Here, we revisit this topic comparing organic and conventional...

Data from: Avoiding tipping points in fisheries management through Gaussian process dynamic programming

Carl Boettiger, Marc Mangel, Stephan Munch, C. Boettiger & S. Munch
Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some...

Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms

Joshua V. Peñalba, Lydia L. Smith, Maria A. Tonione, Chodon Sass, Sarah M. Hykin, Phillip L. Skipwith, James A. McGuire, Rauri C. K. Bowie, Craig Moritz & Jimmy A. McGuire
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized...

Data from: Monocyte recruitment to the dermis and differentiation to dendritic cells increases the targets for Dengue virus replication

Michael A. Schmid & Eva Harris
Dengue virus (DENV) causes the most prevalent arthropod-borne viral disease in humans. Although Aedes mosquitoes transmit DENV when probing for blood in the skin, no information exists on DENV infection and immune response in the dermis, where the blood vessels are found. DENV suppresses the interferon response, replicates, and causes disease in humans but not wild-type mice. Here, we used mice lacking the interferon-α/β receptor (Ifnar–/–), which had normal cell populations in the skin and...

Data from: The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices

Robert Guralnick, Tom Conlin, John Deck, Brian Stucky, Nico Cellinese & Brian J. Stucky
The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the “Darwin Core Triplet”, which is a concatenation of values for institution code, collection code, and catalog number associated with biocollections material. Our aim is not to rehash the challenging discussions regarding which GUID system in theory best supports the biodiversity...

Data from: Genetic divergence is decoupled from ecological diversification in the Hawaiian Nesosydne planthoppers

Kari Roesch Goodman, Stephen C. Welter & George K. Roderick
Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history...

Data from: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote

Gerald Schönknecht, Wei-Hua Chen, Chad M. Ternes, Guillaume G. Barbier, Roshan P. Shrestha, Mario Stanke, Andrea Bräutigam, Brett J. Baker, Jillian F. Banfield, R. Michael Garavito, Kevin Carr, Curtis Wilkerson, Stefan A. Rensing, David Gagneul, Nicholas E. Dickenson, Christine Oesterhelt, Martin J. Lercher & Andreas P. M. Weber
Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, can live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7 Mb genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family...

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  • University of California, Berkeley
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