36 Works

Genome content flat files for comparative genomic analysis of seadragons and relatives

Clayton Small
Seadragons are widely recognized for their derived and novel traits. Research and conservation efforts involving these unique fish species and their relatives have been hindered by a lack of genomic resources. From this project we present full, annotated genomes of leafy and weedy seadragons, which help uncover surprising features of gene family and genome architecture evolution that likely relate to extreme phenotypic traits in seadragons, pipefishes, and seahorses. These genomes are important research resources for...

Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Iliana Bista, Jonathan Wood, Thomas Desvignes, Shane McCarthy, Michael Matschiner, Zemin Ning, Alan Tracey, James Torrance, Ying Sims, William Chow, Michelle Smith, Karen Oliver, Leanne Haggerty, Walter Salzburger, John H. Postlethwait, Kerstin Howe, Melody S. Clark, H. William Detrich, C.-H. Christina Cheng, Eric Miska & Richard Durbin
Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from...

Supplemental File 13- Split Selection Landing Pad (SSLP) Sequences

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
All landing pad sequences along with limited surrounding genomic region used in this study and described in the manuscript

Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone

Matthew Streisfeld, Sean Stankowski, Madeline Chase & Hanna McIntosh
Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine ‘top-down’ and ‘bottom-up’ approaches with demographic modeling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to...

Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

Hope Healey, Susan Bassham & William Cresko
Single cell RNA sequencing (scRNAseq) is a powerful technique that continues to expand across various biological applications. However, incomplete 3’ UTR annotations can impede single cell analysis resulting in genes that are partially or completely uncounted. Performing scRNAseq with incomplete 3’ UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single cell isoform sequencing (ScISOr-Seq) in tandem with scRNAseq can rapidly...

Using GBIF to Demonstrate Colonial Legacies on Biodiversity Data

Ryan S. Mohammed, Melissa Kemp, Michelle J. LeFebvre, Alexis M. Mychajliw, Grace Turner, Kelly Fowler, Michael Pateman, Maria A. Nieves-Colón, Lanya Fanovich, Siobhan B. Cooke, Liliana M. Dávalos, Scott M. Fitzpatrick, Christina M. Giovas, Myles Stokowski & Ashley A. Wrean
Biologists recognize the Caribbean archipelago as a biodiversity hotspot and employ it for their research as a “natural laboratory”, but do not always appreciate that these ecosystems are in fact palimpsests shaped by multiple human cultures over millennia. We discuss two case studies of the Caribbean’s fragmented natural history collections, the effects of differing legislation and governance by the region’s multiple nation states. We use digital natural history specimen data from GBIF to demonstrate how...

Evolutionary causes and consequences of ungulate migration

Joel Abraham, Nathan Upham, Alejandro Damian-Serrano & Brett Jesmer
Ungulate migrations are crucial for maintaining abundant populations and functional ecosystems. However, little is known about how or why migratory behavior evolved in ungulates. To investigate the evolutionary origins of ungulate migration, we employed phylogenetic path analysis using a comprehensive species-level phylogeny of mammals. We found that 95 of 207 extant ungulate species are at least partially migratory, with migratory behavior originating independently in 17 lineages. The evolution of migratory behavior is associated with reliance...

Western Juniper Woodlands climate relations meta analysis

Schyler Reis
These data are based on tree-ring data from the internation tree ring data base and PRISM climate data.

Joint coding of visual input and eye/head position in V1 of freely moving mice dataset

Philip RL Parker, Elliott TT Abe, Emmalyn SP Leonard, Dylan M Martins & Cristopher M Niell
Visual input during natural behavior is highly dependent on movements of the eyes and head, but how information about eye and head position is integrated with visual processing during free movement is unknown, since visual physiology is generally performed under head-fixation. To address this, we performed single-unit electrophysiology in V1 of freely moving mice while simultaneously measuring the mouse’s eye position, head orientation, and the visual scene from the mouse’s perspective. From these measures, we...

Supplemental File 2- Replicate two data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate two.

Supplemental File 1- Replicate one data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate one.

Supplemental File 7- Array 3 profile 1 PX818 Barcode Counts

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing all barcode sequences and frequencies found in array 3 PX818 profile 1 across four individual worms.

Leaf traits predict water-use efficiency in U.S. Pacific Northwest grasslands under rain exclusion treatment

Hilary Rose Dawson, Toby Maxwell, Paul Reed, Scott Bridgham & Lucas Silva
Does drought stress in temperate Pacific Northwest, USA, grasslands alters the relationship between plant structure and function? Here we report data from an experiment focusing on growth form and species traits that affect the critical functions of water- and nutrient-use efficiency in prairie and pasture plant communities. A total of 139 individuals of 12 species (11 genera and four families) were sampled in replicated plots maintained for three years across a 520 km latitudinal gradient...

Data from: Incorporating temporal dynamics to enhance grazing management outcomes for a long-lived species

Loralee Larios & Lauren Hallett
Identifying successful management strategies for long-lived species is challenging, especially in fluctuating environments, because the response of individual vital rates and overall growth rates to management action can vary over time. A demographic approach that isolates the impact of management and environment on individual vital rates, and assesses their importance for growth rate over time, can indicate whether and why a management strategy is successful. Here we take a demographic approach to assess the success...

Supplemental File 4- Replicate four data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate four.

Supplemental File 5- Array 1 PX816 Barcode Count

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing all barcode sequences and frequencies found in array 1 PX816 across six individual worms.

Supplemental File 12- Plasmid Sequences

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
Plasmids used in this study and described in the manuscript

Supplemental File 13- Split Selection Landing Pad (SSLP) Sequences

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
All landing pad sequences along with limited surrounding genomic region used in this study and described in the manuscript

Nutrient addition drives declines in grassland species richness primarily via enhanced species loss

Andrew Muehleisen
Declines in grassland diversity in response to nutrient addition are a general consequence of global change. This decline in species richness may be driven by multiple underlying processes operating at different timescales. Nutrient addition can reduce diversity by enhancing the rate of local extinction via competitive exclusion, or by reducing the rate of colonization by constraining the pool of species able to colonize under new conditions. Partitioning net change into extinction and colonization rates will...

Supplemental File 5- Array 1 PX816 Barcode Count

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing all barcode sequences and frequencies found in array 1 PX816 across six individual worms.

Supplemental File 12- Plasmid Sequences

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
Plasmids used in this study and described in the manuscript

Supplemental File 2- Replicate two data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate two.

Supplemental File 4- Replicate four data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate four.

Supplemental File 3- Replicate three data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate three.

Supplemental File 3- Replicate three data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate three.

Registration Year

  • 2022
    36

Resource Types

  • Dataset
    36

Affiliations

  • University of Oregon
    36
  • Georgia Institute of Technology
    20
  • The Wallace H. Coulter Department of Biomedical Engineering
    20
  • Wayne State University
    2
  • Antiquities, Monuments and Museum Corporation
    1
  • The University of Texas at Austin
    1
  • Princeton University
    1
  • Oregon State University
    1
  • Johns Hopkins University
    1
  • University of Cambridge
    1