73 Works

Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow

Diana Le Duc, Akhil Velluva, Molly Cassatt-Johnstone, Remi-Andre Olsen, Sina Baleka, Chen-Ching Lin, Johannes R. Lemke, John R. Southon, Alexander Burdin, Ming-Shan Wang, Sonja Grunewald, Wilfried Rosendahl, Ulrich Joger, Sereina Rutschmann, Thomas B. Hildebrandt, Guido Fritsch, James A. Estes, Janet Kelso, Love Dalén, Michael Hofreiter, Beth Shapiro & Torsten Schöneberg
Steller’s sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller’s descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller’s sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse...

Data from: Rethinking sustainability in seafood: synergies and trade-offs between fisheries and climate change

Brandi McKuin, Jordan Watson, Stephen Stohs & J. Elliott Campbell
In the manuscript entitled, "Rethinking sustainability in seafood: synergies and trade-offs between fisheries and climate change", we quantified the climate forcing per unit fish protein associated with several different U.S. tuna fishing fleets, among the most important capture fisheries by both volume and value. The fishing fleets include the U.S. purse seine that operates in the Western Central Pacific Fisheries Commission convention area, the U.S. North Pacific albacore surface gear (which includes both troll and...

Effects of insect herbivory on seedling mortality in restored and remnant tropical forest

Andy J. Kulikowski, Rakan A. Zahawi & Karen D. Holl
Insect herbivory is one of the major drivers of seedling mortality in the tropics and influences plant abundances and community composition. Anthropogenic disturbance can alter patterns of insect herbivory with potential consequences on plant communities in restored forests. We planted seedlings of early- and later-stage successional tree species in 13–15-year-old restored and remnant tropical forests. We then either excluded insect herbivores or left seedlings exposed to examine how insect herbivory-affected seedling mortality. Early-successional seedlings experienced...

Data from: Temporal scale of habitat selection for large carnivores: Balancing energetics, risk and finding prey

Anna Nisi, Justin Suraci, Nathan Ranc, Laurence Frank, Alayne Oriol-Cotterill, Steven Ekwanga, Terrie Williams & Christopher Wilmers
1. When navigating heterogeneous landscapes, large carnivores must balance trade-offs between multiple goals, including minimizing energetic expenditure, maintaining access to hunting opportunities, and avoiding potential risk from humans. The relative importance of these goals in driving carnivore movement likely changes across temporal scales, but our understanding of these dynamics remains limited. 2. Here we quantified how drivers of movement and habitat selection changed with temporal grain for two large carnivore species living in human-dominated landscapes,...

CATS tag example deployment

William Gough & David Cade
Biologging tags are capable of capturing high-resolution data from cryptic species that spend a significant portion of their lives in remote or inaccessible environments, such as below the sea surface. The advancement of biologging technologies over the last ~30 years has lead to an explosion of research into the hidden lives of these elusive animals. Information about locomotion, feeding, migratory patterns, reproduction, and metabolism have all been determined using data obtained with biologging tags. CATS...

Southern Cascadia earthquake catalog 2014-July to 2015-October

Travis Alongi
Fault coupling is vital in determining the amount of strain that is accumulated along faults. The magnitude and location of stored elastic strain energy in highly coupled regions has important implications for understanding the full range of slip behavior at plate boundary faults, as well as earthquake and tsunami hazards. We use the temporary dense amphibious array of seismometers offered by the Cascadia Initiative to create a high-resolution catalog of events to examine the spatio-temporal...

Secondary Contact LTREB: Lake metadata

David Post & Eric Palkovacs
This dataset contains metadata for the core lakes of the Secondary Contact LTREB and other lakes that are occasionally sampled by the project.

Data from: Testing applied nucleation as a strategy to facilitate tropical forest recovery

Rakan A. Zahawi, Karen D. Holl, Rebecca J. Cole & J. Leighton Reid
Active forest restoration typically involves planting trees over large areas; this practice is costly, however, and establishing homogeneous plantations may favour the recruitment of a particular suite of species and strongly influence the successional trajectory. An alternative approach is to plant nuclei (islands) of trees to simulate the nucleation model of succession and accelerate natural recovery. We evaluated natural tree recruitment over 4 years in a restoration study replicated at eight former pasture sites in...

Surrounding forest cover dataset 2005

David Morales, R. J. Cole, Karen D. Holl & R. A. Zahawi
Forest cover within 100 and 500 m radii from the center of each experimental plot was hand digitized from ortho-rectified 2005 aerial photographs and comprehensively ground checked. Forest cover spans a range from <1% to 66% within a 100-m radius surrounding the plots and from 9% to 89% in a 500-m radius.

Data from: Density-dependent effects on reproductive output in a capital breeding carnivore, the northern elephant seal (Mirounga angustirostris)

Daniel Costa, Rachel Holser, Daniel Crocker, Patrick Robinson, Gitte McDonald, Melinda Fowler, Jason Hassrick, Luis Hückstädt, Sarah Peterson, Samantha Simmons & Theresa Keates
All organisms face resource limitations that will ultimately restrict population growth, but the controlling mechanisms vary across ecosystems, taxa, and reproductive strategies. Using four decades of data, we examine how variation in the environment and population density affect reproductive outcomes in a capital-breeding carnivore, the northern elephant seal (Mirounga angustirostris). This species provides a unique opportunity to examine the relative importance of resource acquisition and density-dependence on breeding success. Capital breeders accrue resources over large...

Data for: The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understory herbs

Kathleen Kay & Yann Surget-Groba
Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action, and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here,...

Online phylogenetics using parsimony produces slightly better trees and is dramatically more efficient for large SARS-CoV-2 phylogenies than de novo and maximum-likelihood approaches

Bryan Thornlow
Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 datasets do not fit this mould. There are currently over 5 million sequenced SARS-CoV-2...

Numerical simulation of cool hydrothermal processes in the upper volcanic crust beneath a marine sediment pond: North Pond, North Atlantic Ocean

Adam N. Price, Andrew T. Fisher, Philip H. Stauffer & Carl W. Gable
Low temperature hydrothermal systems hosted in the volcanic oceanic crust are responsible for ~20% of Earth's global heat loss. Marine sediment ponds comprise an important type-setting on young ridge flanks where hydrothermal circulation advectively extracts lithospheric heat, but the nature of coupled fluid-heat transport in these settings remains poorly understood. Here we present coupled (fluid-heat) numerical simulations of ocean crustal hydrogeology in and below North Pond, a sediment pond on ~8 Ma seafloor of the...

A comparative study between outcomes of an in-person vs. online introductory field course

Alexandra Race, Maria De Jesus, Roxanne Beltran & Erika Zavaleta
The COVID-19 pandemic has disrupted many standard approaches to STEM education. Particularly impacted were field courses, which rely on specific natural spaces often accessed through shared vehicles. As in-person field courses have been found to be particularly impactful for undergraduate student success in the sciences, we aimed to compare and understand what factors may have been lost or gained during the conversion of an introductory field course to an online format. Using a mixed methods...

Increased frequency of extreme precipitation events in the North Atlantic during the PETM: Observations and theory

William Rush
Climate model simulations of the PETM (Paleocene-Eocene Thermal Maximum) warming have mainly focused on replicating the global thermal response through greenhouse forcing, i.e. CO2, at levels compatible with observations. Comparatively less effort has gone into assessing the skill of models to replicate the response of the hydrologic cycle to the warming, particularly on regional scales. Here we have assembled proxy records of regional precipitation, focusing on the Mid-Atlantic Coasts of North America (New Jersey) and...

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

Alisa Vershinina, Peter Heintzman, Duane Froese, Grant Zazula, Molly Cassatt-Johnstone, Love Dalén, Clio Der Sarkissian, Shelby Dunn, Luca Ermini, Cristina Gamba, Pamela Groves, Joshua Kapp, Daniel Mann, Andaine Seguin-Orlando, John Southon, Mathias Stiller, Matthew Wooller, Gennady Baryshnikov, Dmitry Gimranov, Eric Scott, Elizabeth Hall, Susan Hewitson, Irina Kirillova, Pavel Kosintsev, Fedor Shidlovsky … & Beth Shapiro
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and...

Variation in resting strategies across trophic levels and habitats in mammals

Roxanne Beltran, Ishana Shukla & A. Marm Kilpatrick
Mammals must carefully balance rest with other behaviors that influence fitness (e.g., foraging, finding a mate) while minimizing predation risk. However, factors influencing resting strategies and the degree to which resting strategies are driven by the activities of predators and/or prey remain largely unknown. Our goal was to examine how mammalian resting strategies varied with trophic level, body mass, and habitat. We reviewed findings from 127 publications and classified the resting strategies of terrestrial and...

Heterogeneous genetic basis of age at maturity in salmonid fishes

Charles Waters, Anthony Clemento, Tutku Aykanat, John Garza, Kerry-Ann Naish, Shawn Narum & Craig Primmer
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait...

Data for: Modeling short-term energetic costs of sonar disturbance to cetaceans using high resolution foraging data

Max Czapanskiy, Matthew Savoca, William Gough, Paolo Segre, Danuta Wisniewska, David Cade & Jeremy Goldbogen
Anthropogenic noise is a pervasive and increasing source of disturbance to wildlife. Marine mammals exhibit behavioral and physiological responses to naval sonar and other sound sources. The lost foraging opportunities and elevated locomotor effort associated with sonar disturbance likely carry energetic costs, which may lead to population-level consequences. We modeled the energetic costs associated with behavioral responses using (1) empirical datasets of cetacean feeding rates and prey characteristics and (2) allometry of swimming performance and...

Threatened salmon rely on a rare life history strategy in a warming landscape

Flora Cordoleani, Corey Phillis, Anna Sturrock, Alyssa FitzGerald, George Whitman, Anthony Malkassian, Peter Weber & Rachel Johnson
Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams....

Dataset S1 - Noelaerhabdaceae organic carbon isotope culture data compilation

Samuel Phelps, Gwenn Hennon, Sonya Dyhrman, María Hernández-Limón, Olivia Williamson & Pratigya Polissar
The carbon isotope fractionation in algal organic matter (Ep), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates Ep to changes in cellular carbon demand relative to diffusive CO2 supply, with larger Ep values occurring at lower carbon demand relative to supply (i.e. abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few...

Data from: Factors explaining variability in woody above-ground biomass accumulation in restored tropical forest

Karen D. Holl & Rakan A. Zahawi
Secondary forests comprise an increasing area of the tropics and play an important role in global carbon cycling. We compare above-ground biomass accumulation of both planted and naturally regenerating trees, as well as C in the top soil layer, in three restoration treatments replicated at 14, six to eight year old restoration sites in southern Costa Rica. Restoration strategies include: control (no planting), planting tree islands, and conventional, mixed-species tree plantations. We evaluate the importance...

Data from: Local tropical forest restoration strategies affect tree recruitment more strongly than does landscape forest cover

Karen D. Holl, John Leighton Reid, José Miguel Chaves-Fallas, Federico Oviedo-Brenes & Rakan A. Zahawi
Developing restoration strategies that accelerate natural successional processes and are resource‐efficient is critical to facilitating tropical forest recovery across millions of hectares of deforested lands in the tropics. We compared tree recruitment after a decade in three restoration treatments (natural regeneration, applied nucleation/island tree planting and plantation) and nearby reference forest in the premontane rain forest zone in southern Costa Rica. The study was replicated at 13 sites with a range of surrounding forest cover,...

Restoration interventions mediate tropical tree recruitment dynamics over time

Andy Kulikowski, Rakan Zahawi, Kai Zhu, Leland Werden & Karen Holl
Forest restoration is increasingly heralded as a global strategy to conserve biodiversity and mitigate climate change, yet long-term studies that compare the effects of different restoration strategies on tree recruit demographics are lacking. We measured tree recruit survival and growth annually in three restoration treatments ‒ natural regeneration, applied nucleation, and tree plantations ‒ replicated at 13 sites in southern Costa Rica, and evaluated the changes over a decade. Early-successional seedlings had 14% higher survival...

Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability

Joshua Smith & Sabrina Garcia
Flexible resource investment is a risk-sensitive reproductive strategy where individuals trade resources spent on reproduction for basic metabolic maintenance and survival. This study examined morphological variation in herbivorous sea urchin grazers across a mosaic landscape of macroalgae-dominated habitats interspersed with patches of sea urchin barrens to determine whether sea urchins shift energy allocation in response to food limitation. Extensive underwater surveys of habitat attributes (e.g., sea urchin density, algae cover) were paired with detailed laboratory...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of California, Santa Cruz
  • Organization For Tropical Studies
  • Organization for Tropical Studies
  • Stanford University
  • University of California, Berkeley
  • University of Alaska Fairbanks
  • National Oceanic and Atmospheric Administration
  • University of California, Davis
  • University of California, Merced
  • University of Alberta