553 Works

Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries management

Eleni 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...

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)...

Heterogeneous genetic basis of age at maturity in salmonid fishes

Charles Waters, Anthony Clemento, Tutku Aykanat, John Garza, Kerry-Ann Naish, Shawn Narum & Craig Primmer
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...

Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology

Sean Wu, Penny Hancock, Arnaud Le Menach, Tanya Russell, Thomas Burkot, , Derek Cummings, Kelly Compton, Daniel Citron, John Marshall, Biyonka Liang, Catherine Moyes, Qian Zhang, David Smith, Samson Kiware, Anne Wilson, Thomas Scott, John Henry, Steven Lindsay, Amit Verma & Hector Sanchez C.
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...

Global Tropical Moored Buoy Array: Wind Direction Accuracy Revisited

Howard Paul Freitag, Michael J. McPhaden & Kenneth J. Connell
NOAA Technical Memorandum OAR-PMEL ; 150

Scaling and structural properties of juvenile bull kelp (Nereocystis luetkeana) Data

Stephanie Crofts & Katie Dobkowski
Bull kelp (Nereocystis luetkeana), the only canopy-forming kelp in the Salish Sea, provides primary production in the nearshore subtidal environment and serves as important habitat for economically and ecologically important species. An annual species, each year juvenile bull kelp sporophytes must grow from the hydrodynamically more benign benthos to the water column, where they experience substantial drag at the surface. Because of the differences in morphology and ecology across life stages, and the fact that...

Phylogeny of Citharexyleae

Laura Frost, Nataly O'Leary, Laura Lagomarsino, David Tank & Richard Olmstead
As a family of Neotropical origin and primarily Neotropical distribution, the Verbenaceae are a good but understudied system with which to understand Neotropical evolution. Tribe Citharexyleae comprises three genera: Baillonia, Citharexylum—one of the largest genera in Verbenaceae—and Rehdera. A molecular phylogenetic approach was taken to resolve intergeneric relationships in Citharexyleae and infrageneric relationships in Citharexylum. The phylogeny is used to elucidate character evolution in a widespread, morphologically diverse Neotropical genus. Seven plastid regions, two nuclear...

Longitudinal variation in the nutritional quality of basal food sources and its effect on invertebrates and fish in subalpine rivers

Fen Guo, Nadine Ebm, Stuart Bunn, Michael Brett, Hannes Hager & Martin Kainz
1. There is growing recognition of the importance of food quality over quantity for aquatic consumers. In streams and rivers, most previous studies considered this primarily in terms of the quality of terrestrial leaf litter and importance of microbial conditioning. However, many recent studies suggest that algae are a more nutritional food source for riverine consumers than leaf litter. To date, few studies have quantified longitudinal shifts in the nutritional quality of basal food resources...

Rare missense functional variants at COL4A1 and COL4A2 in sporadic intracerebral hemorrhage

Jaeyoon Chung, Graham Hamilton, Minsup Kim, Sandro Marini, Bailey Montgomery, Jonathan Henry, Art Cho, Devin Brown, Bradford Worrall, James Meschia, Scott Silliman, Magdy Selim, David Tirschwell, Chelsea Kidwell, Brett Kissela, Steven Greenberg, Anand Viswanathan, Joshua Goldstein, Carl Langefeld, Kristiina Rannikmae, Catherine Sudlow, Neshika Samarasekera, Mark Rodrigues, Rustam Salman, James Prendergast … & Christopher Anderson
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...

Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence -- simulation data

Hossein 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, inputs, and output from N isotope global inverse model

Taylor Martin, Karen Casciotti & Francois Primeau
Model code, ancillary input files, and model output related to Martin et al., Global Biogeochemical Cycles in review

Host Factor Experiment (SM001-P)

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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

Host Factor Experiment (SM019-R)

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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.

Host Factor Experiment (IM007-R)

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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.

Host Factor Experiment (IM001-P)

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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

Host Factor Experiment (SM012-R)

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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.

Host Factor Experiment (SCL008-P)

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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...

Host Factor Experiment (IM009-R)

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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.

Host Factor Experiment (SCL005-R)

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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...

Module 22: How Play Helps Math Learning [online module]

Module 23: Math Stereotypes [online module]

On the cross-population generalizability of gene expression prediction models

Kevin L. Keys, Angel C.Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew W. Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. Lenoir, Jimmie Chun Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard & Christopher R. Gignoux
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...

Ichishkíin Sinwit Yakama / Yakima Sahaptin Dictionary: Audio Files

Virginia Beavert & Sharon Hargus
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....

Speciation and gene flow across an elevational gradient in New Guinea kingfishers

Ethan Linck, Benjamin Freeman & John Dumbacher
Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come...

Long-term change in the parasite burden of shore crabs (Hemigrapsus oregonensis and H. nudus) on the northwestern Pacific coast of North America

Jessica 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...

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Affiliations

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