214 Works

Oxygen exposure of common benthic megafauna off San Diego, CA

Ed Parnell
Oxygen decline poses increasing risks to global shelf communities. This study was conducted to measure species oxygen exposures in situ, and to assess risks of low oxygen based on the hypothesis that species risk varies spatially and is dependent on the interaction of shelf oxygen dynamics with habitat pattern, species mobility and tolerance to low oxygen. Here, we report concomitant observations of oxygen, depth, and habitat for the most common benthic and epibenthic megafauna on...

Phylogenomic analysis and morphological data suggest left-right swimming behavior evolved prior to the origin of the pelagic Phylliroidae (Gastropoda: Nudibranchia)

Jessica Goodheart & Heike Wägele
Evolutionary transitions from benthic to pelagic habitats are major adaptive shifts. Investigations into such shifts are critical for understanding the complex interaction between co-opting existing traits for new functions and novel traits that originate during or post-transition. Gastropod mollusks are of particular interest in regard to benthic-pelagic evolutionary transitions, as shifts from benthic to pelagic habitats are uncommon. Phylliroe is one such pelagic lineage in Phylliroidae, a family of holoplanktonic nudibranchs with a highly aberrant...

Data from: Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation

Diana J. Rennison, Seth M. Rudman & Dolph Schluter
The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature....

Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension

Michal Krawczyk, Lorena Raquel Rocha, Viet Anh Nguyen Huu, Claudia Palomino La Torre, Qianlan Xu, Mary Jabari, Robert N. Weinreb & Dorota Skowronska-Krawczyk
Experimental ocular hypertension induces senescence of retinal ganglion cells (RGCs) that mimicks events occurring in human glaucoma. Senescence-related chromatin remodeling leads to profound transcriptional changes including the upregulation of a subset of genes that encode multiple proteins collectively referred to as the senescenceassociated secretory phenotype (SASP). Emerging evidence suggests that the presence of these proinflammatory and matrix-degrading molecules has deleterious effects in a variety of tissues. In the current study, we demonstrated in a transgenic...

Metabolic theory of ecology successfully predicts distinct scaling of ectoparasite load on hosts

Ryan Hechinger, Kate Sheehan & Andrew Turner
The impacts of parasites on hosts and the role that parasites play in ecosystems must be underlain by the load of parasites in individual hosts. To help explain and predict parasite load across broad swaths of species, quantitative theory has been developed based on fundamental relationships between organism size, temperature, and metabolic rate. Here, we elaborate on an aspect of that “scaling theory for parasitism”, and test a previously unexplored prediction, using new data for...

Data from: APPLES: Scalable distance-based phylogenetic placement with or without alignments

Metin Balaban, Shahab Sarmashghi & Siavash Mirarab
Placing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They...

Data from: Sierra Nevada mountain lake microbial communities are structured by temperature, resources, and geographic location

Marika Schulhof, Andrew Allen, Eric Allen, Natalie Mladenov, John McCrow, Natalie Jones, Jessica Blanton, Hamanda Badona Cavalheri, Drishti Kaul, Celia Symons & Jonathan Shurin
Warming, eutrophication (nutrient fertilization) and brownification (increased loading of allochthonous organic matter) are three global trends impacting lake ecosystems. However, the independent and synergistic effects of resource addition and warming on autotrophic and heterotrophic microorganisms are largely unknown. In this study, we investigate the independent and interactive effects of temperature, dissolved organic carbon (DOC, both allochthonous and autochthonous), and nitrogen (N) supply, in addition to the effect of spatial variables, on the composition, richness, and...

Data from: An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Claudius Kratochwil, Andreas Kautt, Alexander Nater, Andreas Härer, Yipeng Liang, Frederico Henning & Axel Meyer
Polymorphisms have fascinated biologists for a long time, but their genetic underpinnings often remained elusive. Here, we aimed to uncover the genetic basis of the gold/dark polymorphism that is eponymous of Midas cichlid fish (Amphilophus spp.) adaptive radiations in Nicaraguan crater lakes. While most Midas cichlids are of the melanic “dark morph”, about 10% of individuals lose their melanic pigmentation during their ontogeny and transition into a conspicuous “gold morph”. Using a new haplotype-resolved long-read...

Photobehavior for octopus (‘Octopus bimaculatus’) and squid (‘Doryteuthis opalescens’) paralarvae during exposure to 9 light irradiance levels and 4 oxygen conditions in trials conducted in April of 2019

Lillian McCormick, Lisa Levin & Nicholas Oesch
This dataset gives the results of photobehavior experiments under different oxygen conditions in larvae of the market squid (‘Doryteuthis opalescens’) and two-spot octopus (‘Octopus bimaculatus’). Photobehavior experiments were conducted to determine whether the impairment of visual physiology observed in marine invertebrate larvae (McCormick et al., 2019) is subsequently affecting visual behavior in marine larvae.

Current status and future strategies for mentoring women in neurology

Christa San Luis Nobleza, Amtul Farheen, Ilena George, Divya Singhal, Regina Troxell, Jyoti Pillai, Logan Schneider, Catherine Lomen-Hoerth, Jennifer Graves & Stefano Sandrone
The American Academy of Neurology's (AAN) 2017 Gender Disparity Report identified improving mentorship as a key intervention to fill the leadership and pay gaps for women in neurology. Here we summarize the literature on mentoring women, provide an outline of ideal components of programs geared toward closing gender gaps, and present a mentoring program for AAN members. The strategies discussed share similarities with those for closing gaps related to race, ethnicity and religion. Developing effective...

PLANT BREEDING PARTNERSHIP: A Metabolic Modeling-Based Strategy to Accelerate the Citrus Genetic Engineering Process

James Borneman
This is a New Investigator proposal led by Cristal Zuniga. The Long-Term Goal of this proposed project is to improve the economics, productivity, and sustainability of U.S. agriculture by using metabolic models to accelerate the engineering process of all crops. To demonstrate the feasibility of this approach, the Objective of this project is to use metabolic models to speed up the growth rate of two specific steps of the citrus engineering process in two commonly...

Data from: High-throughput molecular identification of fish eggs using multiplex suspension bead arrays

Lani U Gleason & Ronald S Burton
The location and abundance of fish eggs provide information concerning the timing and location of spawning activities and can provide fishery-independent estimates of spawning biomass. However, the full value of egg and larval surveys is severely restricted because many species’ eggs and larvae are morphologically similar, making species-level identification difficult. Recent efforts have shown that nearly all species of fish may be identified by mitochondrial DNA (mtDNA) sequences (e.g., via “DNA barcoding”). By taking advantage...

Data from: Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae

Sean W. Graham, Joshua R. Kohn, Brian R. Morton, James E. Eckenwalder & Spencer C.H. Barrett
A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction-site survey) were used to reconstruct the phylogenetic history of the Pickerelweed family Pontederiaceae. The chloroplast data are converging to a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from the three chloroplast data sets were identical or extremely similar in shape to each other, mostly robustly supported and there was no evidence...

Data from: Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral

Flavia Nunes, Richard Norris & Nancy Knowlton
Limited dispersal and connectivity in marine organisms can have negative fitness effects in populations that are small and isolated, but reduced genetic exchange may also promote the potential for local adaptation. Here, we compare the levels of genetic diversity and connectivity in the coral Montastraea cavernosa among both central and peripheral populations throughout its range in the Atlantic. Genetic data from one mitochondrial and two nuclear loci in 191 individuals show that M. cavernosa is...

Registration Year

  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013

Resource Types

  • Dataset
  • Text
  • Output Management Plan


  • University of California, San Diego
  • University of Kentucky
  • Yale University
  • Harvard University
  • University of California, Irvine
  • University of Washington
  • University of California, Santa Barbara
  • University of Toronto
  • University of British Columbia
  • Columbia University