114 Works

Genomics of new ciliate lineages provides insight into the evolution of obligate anaerobiosis - single gene datasets for phylogenomic analysis of anaerobic ciliates (SAL, Ciliophora), protein datasets for mitochondrial pathways prediction, and mitochondrial genomes

Johana Rotterova, Eric Salomaki, Tomas Panek, William Bourland, David Zihala, Petr Taborsky, Virginia Edgcomb, Roxanne Beinart, Martin Kolisko & Ivan Cepicka
Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet, adaptations to low oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrial organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate...

Differential resistance and acclimation of two coral species to chronic nutrient enrichment reflect life history traits

Michael Fox, Craig E. Nelson, Thomas A. Oliver, Zachary A. Quinlan, Kristina Remple, Jess Glanz, Jennifer E. Smith & Hollie M. Putnam
All data and code associated with this manuscript are freely available in the Dryad Digital Repository.

Recent natural variability in global warming weakened phenological mismatch and selection on seasonal timing in great tits (Parus major)

Marcel E. Visser, Melanie Lindner, Phillip Gienapp, Matthew Long & Stephanie Jenouvrier
Climate change has led to phenological shifts in many species, but with large variation in magnitude among species and trophic levels. The poster child example of the resulting phenological mismatches between the phenology of predators and their prey is the great tit (Parus major), where this mismatch led to directional selection for earlier seasonal breeding. Natural climate variability can obscure the impacts of climate change over certain periods, weakening phenological mismatching and selection. Here, we...

Age-by-maternal-age Markov chain with rewards analysis of variance in LRO in rotifers

Silke Van Daalen
This set of data and code files is a supplement to the American Naturalist paper: van Daalen et al. 2021 The contributions of maternal age heterogeneity to variance in lifetime reproductive output It provides the user the matrices (as first presented in Hernandez et al., 2020, PNAS) and the code to reproduce our analysis or apply the methods to their own data. Two multistate, age-by-maternal-age matrices with basic demographic information (survival and transitions, and fertility)...

Data from: Estimating body mass of free-living whales using aerial photogrammetry and 3D volumetrics

Fredrik Christiansen, Mariano Sironi, Michael J. Moore, Matías Di Martino, Marcos Ricciardi, Hunter A. Warick, Duncan J. Irschick, Robert Gutierrez & Marcela M. Uhart
1. Body mass is a key life history trait in animals. Despite being the largest animals on the planet, no method currently exists to estimate body mass of free-living whales. 2. We combined aerial photographs and historical catch records to estimate the body mass of free-living right whales (Eubalaena sp.). First, aerial photogrammetry from unmanned aerial vehicles was used to measure the body length, width (lateral distance) and height (dorso-ventral distance) of free-living southern right...

Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses

Erica Lasek-Nesselquist & Matthew D. Johnson
Recent high-throughput sequencing endeavors have yielded multi-gene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically-rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multi-protein dataset, or the...

Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses

Erica Lasek-Nesselquist & Matthew D. Johnson
Recent high-throughput sequencing endeavors have yielded multi-gene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically-rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multi-protein dataset, or the...

Seasons of Syn

Kristen R. Hunter‐Cevera, Michael G. Neubert, Robert J. Olson, Alexi Shalapyonok, Andrew R. Solow & Heidi M. Sosik
Synechococcus is a widespread and important marine primary producer. Time series provide critical information for identifying and understanding the factors that determine abundance patterns. Here, we present the results of analysis of a 16‐yr hourly time series of Synechococcus at the Martha's Vineyard Coastal Observatory, obtained with an automated, in situ flow cytometer. We focus on understanding seasonal abundance patterns by examining relationships between cell division rate, loss rate, cellular properties (e.g., cell volume, phycoerythrin...

Data from: Singing whales generate high levels of particle motion: implications for acoustic communication and hearing?

T. Aran Mooney, Maxwell B. Kaplan & Marc O. Lammers
Acoustic signals are fundamental to animal communication, and cetaceans are often considered bioacoustic specialists. Nearly all studies of their acoustic communication focus on sound pressure measurements, overlooking the particle motion components of their communication signals. Here we characterized the levels of acoustic particle velocity (and pressure) of song produced by humpback whales. We demonstrate that whales generate acoustic fields that include significant particle velocity components that are detectable over relatively long distances sufficient to play...

Data from: The evolution of marine larval dispersal kernels in spatially structured habitats: analytical models, individual-based simulations, and comparisons with empirical estimates

Allison K. Shaw, Cassidy C. D'Aloia & Peter M. Buston
Understanding the causes of larval dispersal is a major goal of marine ecology, yet most research focuses on proximate causes. Here, we ask how ultimate, evolutionary causes affect dispersal. Building on Hamilton and May's 1977 classic paper (``Dispersal in stable habitats"), we develop analytic and simulation models for the evolution of dispersal kernels in spatially structured habitats. First, we investigate dispersal in a world without edges and find that most offspring disperse as far as...

Data from: Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats

Adam M. Reitzel, Sibel I. Karchner, Diana G. Franks, Brad R. Evans, Diane Nacci, Denise Champlin, Verónica M. Vieira & Mark E. Hahn
Background: The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other “dioxin-like compounds” (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and...

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: Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses Ridgeia piscesae

Liao Li, Scott D. Wankel, Wu Min, Colleen M. Cavanaugh, Peter R. Girguis & Min Wu
Chemoautotrophic symbionts of deep sea hydrothermal vent tubeworms are known to provide their hosts with all their primary nutrition. While studies have examined how chemoautotrophic symbionts provide the association with nitrogen, fewer have examined if symbiont nitrogen metabolism varies as a function of environmental conditions. Ridgeia piscesae tubeworms flourish at Northeastern Pacific vents, occupy a range of microhabitats, and exhibit a high degree of morphological plasticity [e.g. long-skinny (LS) and short-fat (SF) phenotypes] that may...

Tidal dispersion in short estuaries

Adrian Mikhail P. Garcia & W. Rockwell Geyer
The salinity distribution of an estuary depends on the balance between the river outflow, which is seaward, and a dispersive salt flux, which is landward. The dispersive salt flux at a fixed cross-section can be divided into shear dispersion, which is caused by spatial correlations of the cross-sectionally varying velocity and salinity, and the tidal oscillatory salt flux, which results from the tidal correlation between the cross-section averaged, tidally varying components of velocity and salinity....

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