75 Works

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...

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....

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...

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 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...

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,...

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...

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...

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 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...

Microhabitats associated with solar energy development alter demography of two desert annuals

Karen Tanner, Kara Moore-O'Leary, Ingrid Parker, Bruce Pavlik, Sophia Haji & Rebecca Hernandez
Political and economic initiatives intended to increase energy production while reducing carbon emissions are driving demand for solar energy. Consequently, desert regions are now targeted for development of large-scale photovoltaic solar energy facilities. Where vegetation communities are left intact or restored within facilities, ground-mounted infrastructure may have negative impacts on desert-adapted plants because it creates novel rainfall runoff and shade conditions. We used experimental solar arrays in the Mojave Desert to test how these altered...

Determinants of Financial Stress and Recovery during the Great Recession

Joshua Aizenman & Gurnain Kaur Pasricha
In this paper, we explore the link between stress in the domestic financial sector and the capital flight faced by countries in the 2008-9 global crisis. Both the timing of emergence of internal financial stress in developing economies, and the size of the peak-trough declines in the stock price indices was comparable to that in high income countries, indicating that there was no decoupling, even before Lehman Brothers’ demise. Deleveraging of OECD positions seemed to...

Effectiveness of Capital Controls in India: Evidence from the Offshore NDF Market

Michael Hutchison, Gurnain Kaur Pasricha & Nirvikar Singh
This paper examines the effectiveness of international capital controls in India over time by analyzing daily return differentials in the non-deliverable forward (NDF) markets using the self-exciting threshold autoregressive (SETAR) methodology. We begin with a detailed narrative on the evolution of capital controls in India and calculate deviations from covered interest parity utilizing data from the 3-month offshore non-deliverable rupee forward market. We estimate a no-arbitrage band using SETAR where boundaries are determined by transactions...

Data from: Ant–scale mutualism increases scale infestation, decreases folivory, and disrupts biological control in restored tropical forests

Andy J. Kulikowski & Karen Holl
Ant–hemipteran mutualisms can have positive and negative effects on host plants depending on the level of hemipteran infestation and plant protection conferred by ants against folivory. Differential effects of such mutualisms on plant survival are well documented in undisturbed and ant‐invaded systems, but few have explored how anthropogenic disturbance affects interactions between hemipterans and native ant species and what the consequences may be for recovering ecosystems. Within a fragmented landscape in Costa Rica, restored tropical...

Site description

Karen Holl
Descriptions of 15 original sites from Islas project. Used in various publications and described in Holl, K. D., J. L. Reid, R. J. Cole, F. Oviedo-Brenes, J. A. Rosales, and R. A. Zahawi. 2020. Applied nucleation facilitates tropical forest recovery: Lessons learned from a 15-year study. Journal of Applied Ecology 57:2316-2328.

Data from: A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA

Joshua Kapp, Richard Green & Beth Shapiro
We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina’s P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare five ancient DNA extracts...

Bird Frugivore Abundance data from: Applied nucleation facilitates tropical forest recovery

Karen D. Holl, J. Leighton Reid, Rebecca J. Cole, Federico Oviedo‐Brenes, Juan A. Rosales & Rakan A. Zahawi
Applied nucleation, mostly based upon planting tree islands, has been proposed as a cost‐effective strategy to meet ambitious global forest and landscape restoration targets. We review results from a 15‐year study, replicated at 15 sites in southern Costa Rica, that compares applied nucleation to natural regeneration and mixed‐species tree plantations as strategies to restore tropical forest. We have collected data on planted tree survival and growth, woody vegetation recruitment and structure, seed rain, litterfall, epiphytes,...

Data from: Effects of dispersal‐ and niche‐based factors on tree recruitment in tropical wet forest restoration

Leland K. Werden, Karen D. Holl, Juan Abel Rosales, Janelle M. Sylvester & Rakan A. Zahawi
Both dispersal‐ and niche‐based factors can impose major barriers on tree establishment. Our understanding of how these factors interact to determine recruitment rates is based primarily on findings from mature tropical forests, despite the fact that a majority of tropical forests are now secondary. Consequently, factors influencing seed limitation and the seed‐to‐seedling transition (STS) in disturbed landscapes, and how those factors shift during succession, are not well understood. We used a 3.5‐yr record of seed...

Data from: Litterfall and nutrient dynamics shift in tropical forest restoration sites after a decade of recovery

Karen D. Holl, Fernando Casanoves, Rakan A. Zahawi, Danielle Celentano, Diego Delgado & Oscar Lanuza
Multi‐year studies comparing changes in litterfall biomass and nutrient inputs in sites under different restoration practices are lacking. We evaluated litterfall dynamics and nutrient inputs at 5 yr and after a decade of recovery in four treatments (natural regeneration—no planting, plantation—entire area planted, tree islands—planting in patches, and reference forest) at multiple sites in an agricultural landscape in southern Costa Rica. We inter‐planted two native species (Terminalia amazonia and Vochysia guatemalensis) and two naturalized N‐fixing...

Zostera marina microsatellite and environmental data

Erin Foster, Jane Watson, Matthew Lemay, Tim Tinker, James Estes, Rebecca Piercey, Lauren Henson, Carol Ritland, Allyson Miscampbell, Linda Nichol, Margot Hessing-Lewis, Anne Salomon & Chris Darimont
Microsatellite data for Zostera marina, sea otter occupancy information, and environmental data from the west coast of British Columbia, Canada.

Lewontin 1972 The Apportionment of Human Diversity Apportionment Check and Recalculation Winther 2022

Rasmus Grønfeldt Winther
Data and recalculations of Lewontin (1972), per Winther, R.G. 2022. Lewontin (1972). In Lorusso, L and Winther, RG. Remapping Race in a Global Context. London: Routledge. In redoing all of his calculations, I find that Lewontin made calculation errors (including rounding errors or omitting diversity component values) for all the genes he analyzed, and understated the among races diversity component, according to even just his own calculations. I show that “Lewontin’s Distribution” of, respectively, within...

Data from: Reduced aboveground tree growth associated with higher arbuscular mycorrhizal fungal diversity in tropical forest restoration

Ellen K. Holste, Karen D. Holl, Rakan A. Zahawi & Richard K. Kobe
Establishing diverse mycorrhizal fungal communities is considered important for forest recovery, yet mycorrhizae may have complex effects on tree growth depending on the composition of fungal species present. In an effort to understand the role of mycorrhizal fungi community in forest restoration in southern Costa Rica, we sampled the arbuscular mycorrhizal fungal (AMF) community across eight sites that were planted with the same species (Inga edulis, Erythrina poeppigiana, Terminalia amazonia, and Vochysia guatemalensis) but varied...

Data from: Seed dispersal limitations shift over time in tropical forest restoration

J. Leighton Reid, Karen D. Holl & Rakan A. Zahawi
Past studies have shown that tropical forest regeneration on degraded farmlands is initially limited by lack of seed dispersal, but few studies have tracked changes in abundance and composition of seed rain past the first few years after land abandonment. We measured seed rain for 12 months in 10 6–9‐year‐old restoration sites and five mature, reference forests in southern Costa Rica in order to learn (1) if seed rain limitation persists past the first few...

Forest Survey data 2012-2013

Karen Holl
Vegetation composition of 6 representative forest fragments adjacent to restoration study plots in the Islas Project.

Analyzing coastal fog effects on carbon and water fluxes in a California agricultural system using approaches in biometeorology, remote sensing, and plant physiology

Sara Baguskas, Andrew Oliphant, Rachel Clemesha & Michael Loik
In coastal California, the peak growing season of economically important crops is concurrent with fog events, which buffer drought stress during the dry season. Coastal fog patterns are changing, so we quantified its effects on the energy, water, and carbon fluxes of an economically important cropland at multiple spatial and temporal scales. Our study site was a strawberry farm located in the fog-belt of the Salinas Valley, California. We used GOES-satellite total albedo to detect...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text


  • 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