46 Works

Data from: Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease

Timothy R. Sampson, Justine W. Debelius, Taren Thron, Stefan Janssen, Gauri G. Shastri, Zehra Esra Ilhan, Collin Challis, Catherine E. Schretter, Sandra Rocha, Viviana Gradinaru, Marie-Francoise Chesselet, Ali Keshavarzian, Kathleen M. Shannon, Rosa Krajmalnik-Brown, Pernilla Wittung-Stafshede, Rob Knight & Sarkis K. Mazmanian
The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson’s disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology. Antibiotic treatment ameliorates, while microbial re-colonization promotes, pathophysiology in...

Data from: Pollution-tolerant invertebrates enhance greenhouse gas flux in urban wetlands

Andrew S. Mehring, Perran L.M. Cook, Victor Evrard, Stanley B. Grant, Lisa A. Levin & Perran L. M. Cook
One of the goals of urban ecology is to link community structure to ecosystem function in urban habitats. Pollution-tolerant wetland invertebrates have been shown to enhance greenhouse gas (GHG) flux in controlled laboratory experiments, suggesting that they may influence urban wetland roles as sources or sinks of GHG. However, it is unclear if their effects can be detected in highly variable conditions in a field setting. Here we use an extensive dataset on carbon dioxide...

Data from: Climate and landscape drive the pace and pattern of conifer encroachment into subalpine meadows

Kaitlin C. Lubetkin, Anthony Leroy Westerling & Lara M. Kueppers
Mountain meadows have high biodiversity and help regulate stream water release following the snowmelt pulse. However, many meadows are experiencing woody plant encroachment, threatening these ecosystem services. While there have been field surveys of individual meadows and remote sensing-based landscape-scale studies of encroachment, what is missing is a broad scale, ground-based study to understand common regional drivers, especially at high elevations, where land management has often played a less direct role. With this study we...

Data from: Suitability of Laurentian Great Lakes for invasive species based on global species distribution models and local habitat

Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng & John M. Drake
Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model...

Data from: Do impacts of an invasive nitrogen-fixing shrub on Douglas-fir and its ectomycorrhizal mutualism change over time following invasion?

Sara Grove, Ingrid M. Parker & Karen A. Haubensak
1. Impacts of invasive species may change in magnitude and even direction with invasion age. Impacts could increase as the population increases, individuals grow in size, and ecological changes accumulate. 2. We used a chronosequence approach to characterize the development of soil impacts over time following the invasion of Cytisus scoparius, a widespread nitrogen-fixing shrub thought to limit reforestation success. In a greenhouse experiment, we evaluated how abundance of ectomycorrhizal fungi, Douglas-fir performance, and leaf...

Data from: History cleans up messes: the impact of time in driving divergence and introgression in a tropical suture zone

Sonal Singhal & Ke Bi
Contact zones provide an excellent arena in which to address questions about how genomic divergence evolves during lineage divergence. They allow us to both infer patterns of genomic divergence in allopatric populations isolated from introgression and to characterize patterns of introgression after lineages meet. Thusly motivated, we analyze genome-wide introgression data from four contact zones in three genera of lizards endemic to the Australian Wet Tropics. These contact zones all formed between morphologically cryptic lineage-pairs...

Data from: Fit for genomic and proteomic purposes: sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue

Anna Yakovleva, Jordan L. Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lange, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony & Jonathan Lang
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules. We conducted a systematic examination of nucleic...

Data from: Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia

Nicole L. Crane, Peter Nelson, Avigdor Abelson, Kristin Precoda, , Giacomo Bernardi & Michelle Paddack
The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1–oceanic...

Data from: Form–function relationships in a marine foundation species depend on scale: a shoot to global perspective from a distributed ecological experiment

Jennifer L. Ruesink, John J. Stachowicz, Pamela L. Reynolds, Christoffer Boström, Mathieu Cusson, James Douglass, Johan Eklöf, Aschwin H. Engelen, Masakazu Hori, Kevin Hovel, Katrin Iken, Per-Olav Moksnes, Masahiro Nakaoka, Mary I. O'Connor, Jeanine L. Olsen, Erik E. Sotka, Matthew A. Whalen & Emmett J. Duffy
Form-function relationships in plants underlie their ecosystem roles in supporting higher trophic levels through primary production, detrital pathways, and habitat provision. For widespread, phenotypically-variable plants, productivity may differ not only across abiotic conditions, but also from distinct morphological or demographic traits. A single foundation species, eelgrass (Zostera marina), typically dominates north temperate seagrass meadows, which we studied across 14 sites spanning 32-61° N latitude and two ocean basins. Body size varied by nearly two orders...

Data from: Differential persistence favors habitat preferences that determine the distribution of a reef fish

John E. Majoris, Cassidy C. D'Aloia, Robin K. Francis & Peter M. Buston
A central focus of population ecology is understanding what factors explain the distribution and abundance of organisms within their range. This is a key issue in marine systems, where many organisms produce dispersive larvae that develop offshore before returning to settle on benthic habitat. We investigated the distribution of the neon goby, Elacatinus lori, on sponge habitat and evaluated whether variation in the persistence of recently settled individuals (i.e., settlers) among different sponge types can...

Data from: Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales

Sydney I. Glassman, Ian J. Wang & Thomas D. Bruns
Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree “islands” to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly-related, congeneric pine trees established at varying distances from each other and the forest edge, allowing...

Data from: Microhaplotypes provide increased power from short-read DNA sequences for relationship inference

Diana S. Baetscher, Anthony J. Clemento, Thomas C. Ng, Eric C. Anderson & John C. Garza
The accelerating rate at which DNA sequence data is now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by high-throughput sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens)...

Data from: Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern

Diana S. Baetscher, Daniel J. Hasselman, Kerry Reid, Eric P. Palkovacs & John Carlos Garza
Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high-throughput DNA sequencing to discover SNPs and...

Data from: Are extraversion and openness indicators of a slow life history strategy?

Joseph H. Manson
Theory and data generally concur that a slower Life History Strategy (LHS) is associated with higher Conscientiousness, Agreeableness and Emotional Stability. Whether Extraversion and Openness are indicators of a slow LH, or whether they include both fast and slow LH components, remains unresolved. I addressed these questions in two studies: one of university students observed via periodic brief audio recordings during 72 hours of their daily lives, and the second a re-analysis of data from...

Data from: Integrating lipid storage into general representations of fish energetics

Benjamin T. Martin, Ron Heintz, Eric M. Danner & Roger M. Nisbet
Fish, even of the same species, can exhibit substantial variation in energy density (energy per unit wet weight). Most of this variation is due to differences in the amount of storage lipids. In addition to their importance as energy reserves for reproduction and for survival during unfavourable conditions, the accumulation of lipids represents a large energetic flux for many species, so figuring out how this energy flux is integrated with other major energy fluxes (growth,...

Data from: Genetic assignment with isotopes and habitat suitability (GAIAH), a migratory bird case study

Kristen C. Ruegg, Eric C. Anderson, Ryan J. Harrigan, Kristina L. Paxton, Jeffrey F. Kelly, Frank Moore & Thomas B. Smith
1. Identifying migratory connections across the annual cycle is important for studies of migrant ecology, evolution, and conservation. While recent studies have demonstrated the utility of high-resolution SNP-based genetic markers for identifying population-specific migratory patterns, the accuracy of this approach relative to other intrinsic tagging techniques has not yet been assessed. 2. Here, using a straightforward application of Bayes' Rule, we develop a method for combining inferences from high-resolution genetic markers, stable isotopes, and habitat...

Data from: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees

Michael G. Branstetter, Bryan N. Danforth, James P. Pitts, Brant C. Faircloth, Philip S. Ward, Matthew L. Buffington, Michael W. Gates, Robert R. Kula & Seán G. Brady
The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing...

Data from: Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient

Nicholas J. Kooyers, Brooke James & Benjamin K. Blackman
Closely related species may evolve to coexist stably in sympatry through niche differentiation driven by in situ competition, a process termed character displacement. Alternatively, past evolution in allopatry may have already sufficiently reduced niche overlap to permit establishment in sympatry, a process called ecological sorting. The relative importance of each process to niche differentiation is contentious even though they are not mutually exclusive and are both mediated via multivariate trait evolution. We explore how competition...

Data from: The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

Henrik Krehenwinkel, Marisa Fong, Susan Kennedy, Edward Greg Huang, Suzuki Noriyuki, Luis Cayetano & Rosemary Gillespie
PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias...

Data from: Genetic basis of between-individual and within-individual variance of docility

Julien G.A. Martin, Enrico Pirottay, Matthew B. Petellez, Daniel T. Blumstein, J. G. A. Martin, E. Pirotta & M. B. Petelle
Between-individual variation in phenotypes within a population is the basis of evolution. However, evolutionary and behavioural ecologists have mainly focused on estimating between-individual variance in mean trait and neglected variation in within-individual variance, or predictability of a trait. In fact, an important assumption of mixed-effects models used to estimate between-individual variance in mean traits is that within-individual residual variance (predictability) is identical across individuals. Individual heterogeneity in the predictability of behaviours is a potentially important...

Data from: Seasonal variation in daily patterns of social contacts in the European badger Meles meles

Matthew J. Silk, Nicola Weber, Lucy C. Steward, Richard J. Delahay, Darren P. Croft, David J. Hodgson, Mike Boots & Robbie A. McDonald
Social interactions among hosts influence the persistence and spread of infectious pathogens. Daily and seasonal variation in the frequency and type of social interactions will play an important role in disease epidemiology and, alongside other factors, may have an influence on wider disease dynamics by causing seasonal forcing of infection, especially if the seasonal variation experienced by a population is considerable. We explored temporal variation in within-group contacts in a high-density population of European badgers...

Data from: Genetic coupling of female mate choice with polygenic ecological divergence facilitates stickleback speciation

Rachael A. Bay, Matthew E. Arnegard, Gina L. Conte, Jacob Best, Nicole L. Bedford, Shaugnessy R. McCann, Matthew E. Dubin, Yingguang Frank Chan, Felicity C. Jones, David M. Kingsley, Dolph Schluter & Catherine L. Peichel
Ecological speciation with gene flow is widespread in nature, but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, “genetic coupling”) can facilitate speciation. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic...

Data from: Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment

Paul F. Gugger, Christina T. Liang, Victoria L. Sork, Paul Hodgskiss & Jessica W. Wright
Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, both in current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single-nucleotide polymorphisms from...

Data from: Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

Erin Conlisk, Cristina Castanha, Matthew J. Germino, Thomas T. Veblen, Jeremy M. Smith & Lara M. Kueppers
1. Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long lifespans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively. 2. Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two...

Data from: The evolution of feather coloration and song in Old World orioles (genus Oriolus)

Beata Matysiokova, Nicholas Friedman, Lucia Turčoková & Vladimir Remes
What is the tempo and mode of evolution – how fast and in what pattern do traits evolve – is a major question of evolutionary biology. Here we studied patterns of evolutionary change in visual and acoustic signals in Old World orioles. Since producing multiple signals may be costly, we also tested whether there was an evolutionary trade-off between the elaboration of those two types of signals. We studied 30 Oriolus taxa using comparative methods...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of California System
  • University of California, Berkeley
  • Southwest Fisheries Science Center
  • University of Alaska Fairbanks
  • University of Colorado Boulder
  • University of California, Irvine
  • University of Michigan-Ann Arbor
  • University of Virginia
  • University of Gothenburg
  • Lawrence Berkeley National Laboratory