Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait...
Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)Adam Leache, Daniel Portik, Danielle Rivera, Mark-Oliver Rodel, Johannes Penner, Václav Gvoždík, Eli Greenbaum, Gregory Jongsma, Caleb Ofori-Boateng, Marius Burger, Edem Eniang, Rayna Bell & Matthew Fujita
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA)...
Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries managementEleni L. Petrou
The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise, and where many species synchronize their reproduction to seasonal cycles of planktonic productivity. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across...
Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed...
NOAA Technical Memorandum OAR-PMEL ; 150
Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence -- simulation dataHossein Parishani, Michael Pritchard, Christopher Bretherton, Matthew Wyant & Marat Khairoutdinov
This data set contains the simulation outputs used in the study summarized below: Systematic biases in the representation of boundary layer (BL) clouds are a leading source of uncertainty in climate projections. A variation on superparameterization (SP) called ‘‘ultraparameterization’’ (UP) is developed, in which the grid spacing of the cloud-resolving models (CRMs) is fine enough (250x20 m) to explicitly capture the BL turbulence, associated clouds, and entrainment in a global climate model capable of multiyear...
Model code, ancillary input files, and model output related to Martin et al., Global Biogeochemical Cycles in review
Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics.General Design: 20 week-old C57Bl6 mice; ThreeDoses = 1E2, 1E3,1E4 and 1E5 (PFU); Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks
Purpose: To obtain lung samples from Tnfrsf1b knock out mutant mice infected with SARS MA15 virus for transcriptional analyses. Details: Time Points = days 4 and 7 post-infection; 2-3 replicate mice for each condition; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu.
Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG4/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^3 and 10^4 PFU.
Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics.General Design: 20 week-old C57Bl6 mice; ThreeDoses = 1E2, 1E3, & 1E4 (PFU); Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks
Purpose: To obtain lung samples from C57BL6 mice infected with SARS MA15 and deltaORF6 mutant viruses for transcriptional analysis. Details: Time Points = 1, 2, 4 and 7 days post infection; 2-3 replicates for infected and mock mice; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu.
Purpose: To obtain samples for transcriptional and proteomic analysis using wild type icSARS CoV and icSARS ExoNI and icSARS dNSP16 mutants in 2B-4 cells/sorted Calu-3 cells with high ACE2 expression. Details: Time Points = 0, 7, 12, 24, 36, 48, 60 and 72h post infection (Note: only 0, 24, 48 and 72hr samples analysed for proteomics); Done in triplicate for RNA and quadruplicate for protein; Replicates are defined as 3 or 4 different wells, plated...
Purpose: To obtain lung samples from C57BL6 mice infected with A/CA/04/2009 (H1N1) or, mouse-adapted A/CA/04/2009 (H1N1) virus for transcriptional analysis. Details: Time Points = 1, 3 and 5 days post-infection; 2-3 replicates for infected and mock mice; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^6 pfu.
Purpose: To obtain samples for transcriptional and proteomic analysis using wild type and icSARS delta ORF6 virus in 2B-4 cells/sorted Calu-3 cells with high ACE2 expression. Details: Time Points = 0, 3, 7, 12, 24, 30, 36, 48, 54, 60 and 72h post infection; Done in triplicate for both RNA and protein; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks...
The genetic control of gene expression is a core component of human physiology. For the past several years, transcriptome-wide association studies have leveraged large datasets of linked genotype and RNA sequencing information to create a powerful gene-based test of association that has been used in dozens of studies. While numerous discoveries have been made, the populations in the training data are overwhelmingly of European descent, and little is known about the generalizability of these models...
Sahaptin, or Ichishkíin Sínwit (literally, "this language"), is a Plateau Penutian language spoken in south-central Washington and northern Oregon. This dictionary documents the dialect of Sahaptin that is spoken by the Yakama people. Ichishkíin Sínwit Yakama / Yakima Sahaptin Dictionary is the first modern published dictionary of any Sahaptin dialect. The dictionary is divided into three sections: a Sahaptin-English section; an English-Sahaptin section; and a section listing roots used in the formation of Sahaptin words....
Objective To test the genetic contribution of rare missense variants in COL4A1 and COL4A2 in which common variants are genetically associated with sporadic intracerebral hemorrhage (ICH), we performed rare variant analysis in multiple sequencing data for the risk for sporadic ICH. Methods We performed sequencing across 559Kbp at 13q34 including COL4A1 and COL4A2 among 2,133 individuals (1,055 ICH cases; 1,078 controls) in US-based and 1,492 individuals (192 ICH cases; 1,300 controls) from Scotland-based cohorts, followed...
Background: Literature on multi-disciplinary healthcare team interventions to improve quality and safety of care in acute hospital contexts tends to focus on evaluating the success of the intervention by assessing patient outcomes. In contrast, there is little focus on the team who delivered the intervention, how the team worked to deliver the intervention or the context in which it was delivered. In practice, there is a poor understanding of why some interventions work and are...
Resource allocation to a structural biomaterial: induced production of byssal threads decreases growth of a marine musselEmily Roberts, Laura Newcomb, Michelle McCartha, Katie Harrington, Sam LaFramboise, Emily Carrington & Kenneth Sebens
1. Specialized mechanical structures produced by organisms provide crucial fitness advantages. The energetic cost associated with producing these structural materials and the resulting energetic trade-off with growth, however, is rarely quantified. We evaluate resource allocation to structural material production within the context of an energetic framework by combining an experimental manipulation with an energetic model. 2. Mytilid bivalves produce byssus, a network of collagen-like threads that tethers individuals to hard substrate. We hypothesized that a...
Long-term change in the parasite burden of shore crabs (Hemigrapsus oregonensis and H. nudus) on the northwestern Pacific coast of North AmericaJessica Quinn, Sarah Lee, Duncan Greeley, Alyssa Gehman, Armand Kuris & Chelsea Wood
The abundances of free-living species have changed dramatically in recent decades, but little is known about change in the abundance of parasitic species. We investigated whether populations of several parasites have shifted over time in two shore crab hosts, Hemigrapsus oregonensis and H. nudus, by comparing the prevalence and abundance of three parasite taxa in a historical dataset (1969–1970) to contemporary parasite abundance (2018–2020) for hosts collected from 11 intertidal sites located from Oregon, USA...
Interactions among terrestrial carnivores involve a complex interplay of competition, predation, and facilitation via carrion provisioning, and these negative and positive pathways may be closely linked. Here, we developed an integrative framework and synthesized data from 256 studies of intraguild predation, scavenging, kleptoparisitism, and resource availability to examine global patterns of suppression and facilitation. Large carnivores were responsible for one third of mesocarnivore mortality (n = 1,581 individuals), and intraguild mortality rates were superadditive, increasing...
Supplemental Tables for Heal et al: Marine community metabolomes carry fingerprints of phytoplankton community compositionKatherine Heal
Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here we compare 313 polar metabolites in 21 cultured phytoplankton...
University of Washington535
Oregon State University19
University of California, Berkeley15
University of British Columbia13
University of Montana10
Burke Museum of Natural History and Culture9
University of Minnesota9
United States Department of Agriculture8