51 Works

Data from: Biodiversity response to natural gradients of multiple stressors on continental margins

Erik A. Sperling, Christina A. Frieder & Lisa A. Levin
Sharp increases in atmospheric CO2 are resulting in ocean warming, acidification and deoxygenation that threaten marine organisms on continental margins and their ecological functions and resulting ecosystem services. The relative influence of these stressors on biodiversity remains unclear though, as well as the threshold levels for change and when secondary stressors become important. One strategy to interpret adaptation potential and predict future faunal change is to examine ecological shifts along natural gradients in the modern...

Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

Stephen A. Smith, Casey W. Dunn, Nerida G. Wilson, Freya E. Goetz, Caitlin Feehery, Sónia C. S. Andrade, Greg W. Rouse & Gonzalo Giribet
Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among animals only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or...

Data from: Familial social structure and socially-driven genetic differentiation in Hawaiian short-finned pilot whales

Amy M. Van Cise, Karen. K. Martien, Sabre D. Mahaffy, Robin W. Baird, Daniel L. Webster, James H. Fowler, Erin M. Oleson & Phillip A. Morin
Social structure can have a significant impact on divergence and evolution within species, especially in the marine environment, which has few environmental boundaries to dispersal. On the other hand, genetic structure can affect social structure in many species, through an individual preference toward associating with relatives. One social species, the short-finned pilot whale (Globicephala macrorhynchus), has been shown to live in stable social groups for periods of at least a decade. Using mitochondrial control sequences...

Millennial-scale change in Caribbean coral reef ecosystem structure and the role of human and natural disturbance

Katie Cramer, Aaron O'Dea, Jill Leonard-Pingel & Richard Norris
Caribbean coral reefs have transformed into algal-dominated habitats over the past half-century, but the role of specific anthropogenic drivers is unresolved due to the lack of ecosystem-level data predating human disturbance. To better understand the extent and causes of long-term Caribbean reef declines, we produced a continuous 3,000-year record of the ecosystem state of three reefs in Bocas del Toro, Caribbean Panama. From fossils and sediments obtained from reef matrix cores, we tracked changes in...

Niche differences in co-occurring cryptic coral species (Pocillopora spp.)

Erika Johnston, Alex Wyatt, James Leichter & Scott Burgess
Cryptic species that are morphologically similar co-occur because either the rate of competitive exclusion is very slow, or because they are not, in fact, ecologically similar. The processes that maintain cryptic local diversity may, therefore, be particularly subtle and difficult to identify. Here, we uncover differences among several cryptic species in their relative abundance across a depth gradient within a dominant and ecologically important genus of hard coral, Pocillopora. From extensive sampling unbiased towards morphological...

Modeling and Monitoring Submerged Prehistoric Sites during Offshore Sand Dredging and Implications for the Study of Early Holocene Coastal Occupation of Southern California

John Hildebrand & Andrew York
Beach sand dredging projects off the coast of San Diego County in Southern California provide data for improved understanding of the strategraphic setting for early Holocene sediments and the potential for offshore presence of buried archaeological materials. Geophysical data, core sediments, and analysis of recovered fossils allowed models to be developed for six offshore borrow sites within drown river valleys. These site-specific models were tested during dredging operations, and the dredge spoil was monitored for...

Data from: New approaches to ceramic use and discard: cooking pottery from the Peruvian Andes in ethnoarchaeological perspective

John A. Hildebrand & Melissa B. Hagstrum
Ethnoarchaeological data from contemporary Wanka villages in the Mantaro Valley of the Peruvian Andes provide new perspectives on the use and discard of ceramic cooking vessels. We present a regional survey of ceramic vessel use and discard with household consumption as the focus of study. A mathematical model determines vessel uselife from the age distribution of in-use vessels. We examine the number of vessels per household, their volume, their uselife, and their reported discard. A...

Climate, snow, and soil moisture data set for the Tuolumne and Merced River watersheds, California, USA

James Roche, Robert Rice, Xiande Meng, Daniel Cayan, Mike Dettinger, Douglas Alden, Sarina Patel, Megan Mason, Martha Conklin & Roger Bales
UCM sites. Snow depth, soil moisture and soil temperature are measured near the Merced Grove, Gin Flat, Smoky Jack Creek, and Olmsted Quarry with a distributed array of 6-7 sensor nodes at each location. Snow depth is measured in the open, at the drip edge and under canopies, as well as 3-4 other sites representative of an area of 1-2 hectares. Soil moisture and temperature are measured at 10, 30, 60 and 90 cm depths...

Data from: Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago

Jean-Baptiste Jouffray, Magnus Nyström, Albert V. Norström, Ivor D. Williams, Lisa M. Wedding, John N. Kittinger & Gareth J. Williams
Loss of coral reef resilience can lead to dramatic changes in benthic structure, often called regime shifts, which significantly alter ecosystem processes and functioning. In the face of global change and increasing direct human impacts, there is an urgent need to anticipate and prevent undesirable regime shifts and, conversely, to reverse shifts in already degraded reef systems. Such challenges require a better understanding of the human and natural drivers that support or undermine different reef...

Surface deformation associated with fractures near the 2019 Ridgecrest earthquake sequence

Xiaohua Xu, David T. Sandwell, Lauren A. Ward, Chris W. D. Milliner, Bridget R. Smith-Konter, Peng Fang & Yehuda Bock
Contemporary earthquake hazard models hinge on an understanding of how strain is distributed in the crust and the ability to precisely detect millimeter-scale deformation over broad regions of active faulting. Satellite radar observations revealed hundreds of previously unmapped linear strain concentrations (or fractures) surrounding the 2019 Ridgecrest earthquake sequence. We documented and analyzed displacements and widths of 169 of these fractures. Although most fractures are displaced in the direction of the prevailing tectonic stress (prograde),...

Facultative chemosynthesis in a deep-sea anemone from hydrothermal vents in the Pescadero Basin, Gulf of California

Shana Goffredi, Cambrie Motooka, David Fike, Luciana Gusmão, Ekin Tilic, Greg Rouse & Estefanía Rodríguez
Background Numerous deep-sea invertebrates have formed symbiotic associations with internal chemosynthetic bacteria in order to harness inorganic energy sources typically unavailable to most animals. Despite success in nearly all marine habitats and their well-known associations with photosynthetic symbionts, Cnidaria remain without a clear dependence on hydrothermal vents and chemosynthetic bacterial symbionts specifically. Results A new chemosynthetic symbiosis between the sea anemone Ostiactis pearseae (Daly & Gusmão, 2007) and intracellular bacteria was discovered at ~3700 m...

Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities

Thiago Lima, Ricardo Pereira, Ronald Burton, Tessa Pierce & Lin Chao
Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genome, causing inviability, sterility or low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids...

Climatology of Solomon Sea currents, temperature and salinity measured by glider

William S. Kessler & Hristina G. Hristova
The Solomon Sea carries the equatorward western boundary current of the South Pacific, a principal pathway of subtropical-equatorial communication. This climatological Solomon Sea velocity dataset is derived from more than a decade of Spray glider missions in the Solomon Sea providing measurements of temperature, salinity and vertically-averaged over the dive-depth horizontal velocity. Only the segments of glider missions making complete transects between Papua New Guinea (PNG) and the Solomon Islands (SOL) are considered. All data...

Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character’s evolution: R scripts and simulated trees

Jeremy Wilson, Nicolás Mongiardino Koch & Martín Ramírez
All R scripts used in this study, and the set of simulated phylogenetic trees used in the study. 1. Modern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character’s evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed.2. In this study, we...

Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Nicolás Mongiardino Koch, Jeffrey R Thompson, Avery S Hatch, Marina F McCowin, A Frances Armstrong, Simon E Coppard, Felipe Aguilera, Omri Bronstein, Andreas Kroh, Rich Mooi & Greg W Rouse
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ eighteen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise...

Sea surface temperature from multiple in situ sensors on MISO-BOB 2019 research cruise

Simon de Szoeke
Sea surface temperature (SST) was measured by several instruments deployed from the research vessel Sally Ride in the Bay of Bengal for the Monsoon Intraseasonal Oscillations in the Bay of Bengal (MISO-BOB) 2019 field experiment. This data set presents 1 minute averages of 3 m SST from the Scripps Institution of Oceanography Fast Current-Temperature-Depth sounder (FCTD), 0.2 m SST from the Oregon State University SurfOtter, and 0.1 m SST from a sensor attached to a...

Data from: Before platelets: the production of platelet activating factor during growth and stress in a basal marine organism

Ines Galtier D’Auriac, Robert A. Quinn, Heather Maughan, Louis-Felix Nothias, Mark Little, Clifford A. Kapono, Ana Cobian Guemes, Brandon T. Reyes, Kevin Green, Steven D. Quistad, Matthieu Leray, Jennifer E. Smith, Pieter C. Dorrestein, Forest Rohwer, Dimitri D. Deheyn, Aaron C. Hartmann, Ana Cobian & Ines Galtier D'Auriac
Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecules, PAF and Lyso-PAF biosynthesis was quantified in conditions known to stimulate PAF production in mammals (tissue growth and exposure to elevated levels of ultraviolet light) and in conditions...

Data from: Adaptation to a latitudinal thermal gradient within a widespread copepod species: the contributions of genetic divergence and phenotypic plasticity

Ricardo J. Pereira, Matthew C. Sasaki & Ronald S. Burton
Understanding how populations adapt to heterogeneous thermal regimes is essential for comprehending how latitudinal gradients in species diversification are formed, and how taxa will respond to ongoing climate change. Adaptation can occur by innate genetic factors, by phenotypic plasticity, or by a combination of both mechanisms. Yet, the relative contribution of such mechanisms to large-scale latitudinal gradients of thermal tolerance across conspecific populations remains unclear. We examine thermal performance in 11 populations of the intertidal...

Data from: Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod Tigriopus californicus

Thiago G. Lima, Ronald S. Burton & Christopher Scott Willett
The evolution of intrinsic postzygotic isolation can be explained by the accumulation of Dobzhansky-Muller incompatibilities (DMI). Asymmetries in the levels of hybrid inviability and hybrid sterility are commonly observed between reciprocal crosses, a pattern that can result from the involvement of uniparentally inherited factors. The mitochondrial genome is one such factor that appears to participate in DMI in some crosses but the frequency of its involvement versus biparentally inherited factors is unclear. Here we assess...

Emperor penguin air sac oxygen

Paul Ponganis, Cassondra Williams, Max Czapanskiy, Jason John, Judy St. Leger & Miriam Scadeng
Some marine birds and mammals can perform dives of extraordinary duration and depth. Such dive performance is dependent on many factors, including total body oxygen (O2) stores. For diving penguins, the respiratory system (air sacs and lungs) constitutes 30-50% of the total body O2 store. To better understand the role and mechanism of parabronchial ventilation and O2 utilization in penguins both on the surface and during the dive, we examined air sac partial pressures of...

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: The curious case of Hermodice carunculata (Annelida: Amphinomidae): evidence for genetic homogeneity throughout the Atlantic Ocean and adjacent basins

Joseph B. Ahrens, Elizabeth Borda, Rômulo Barroso, Paulo C. Paiva, Alexandra M. Campbell, Alexander Wolf, Maggy M. Nugues, Greg W. Rouse & Anja Schulze
Over the last few decades, advances in molecular techniques have led to the detection of strong geographic population structure and cryptic speciation in many benthic marine taxa, even those with long-lived pelagic larval stages. Polychaete annelids, in particular, generally show a high degree of population divergence, especially in mitochondrial genes. Rarely have molecular studies confirmed the presence of ‘cosmopolitan’ species. The amphinomid polychaete Hermodice carunculata was long considered the sole species within its genus, with...

Co-occurrence of beaked whale strandings and naval sonar in the Mariana Islands, Western Pacific

Anne Simonis, Robert Brownell, Bruce Thayre, Jennifer Trickey, Erin Oleson, Roderick Huntington & Simone Baumann-Pickering
Mid-frequency active sonar (MFAS), used for antisubmarine warfare (ASW), has been associated with multiple beaked whale (BW) mass stranding events. Multinational naval ASW exercises have utilized MFAS offshore of the Mariana Archipelago semi-annually since 2006. We report BW and MFAS acoustic activity near the islands of Saipan and Tinian from March 2010 through November 2014. Signals from Cuvier’s (Ziphius cavirostris) and Blainville’s beaked whales (Mesoplodon densirostris), and a third unidentified BW species were detected throughout...

Data from: Strong selective effects of mitochondrial DNA on the nuclear genome

Timothy Healy & Ronald Burton
Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod...

Registration Year

  • 2022
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Resource Types

  • Dataset


  • Scripps Institution of Oceanography
  • University of California, San Diego
  • Stanford University
  • University of Hawaii at Manoa
  • Monterey Bay Aquarium Research Institute
  • Harvard University
  • Leibniz Center for Tropical Marine Ecology
  • Dalhousie University
  • Southwest Fisheries Science Center
  • San Diego State University