69 Works

Female Breeding Histories at Año Nuevo

R Condit, Joanne Reiter, Patricia Morris & Burney Le Boeuf
The elephant seal (Mirounga angustirostris) breeding colony at Año Nuevo, California, was founded in 1961, and since monitored closely until the present. Since 1968 a research group at the University of California, Santa Cruz, has studied it in detail. Individually identified females were monitored during the breeding season, and pupping records of many throughout their lifetimes were assembled. We address here the maximum reproductive success of females using the lifetime breeding histories. Females lived to...

Sperm morphology and count vary with fine-scale changes in local density in a wild lizard population

Matthew C Kustra, Ariel F Kahrl, Aaron M Reedy, Daniel A Warner & Robert M Cox
Given that sperm production can be costly, theory predicts that males should optimally adjust the quantity and/or quality of their sperm in response to their social environment to maximize their paternity success. Although experiments demonstrate that males can alter their ejaculates in response to manipulations of the social environment and studies show that ejaculate traits covary with social environment across populations, it is unknown whether individual variation in sperm traits corresponds to natural variation found...

Interspecific and intra-shell stable isotope variation among the Red Sea giant clams

Daniel Killam, Ryan Thomas, Matthew Clapham & Tariq Al-Najjar
The Gulf of Aqaba is home to three giant clam species with differing ecological niches and levels of photosymbiotic activity. Giant clams grow a two-layered shell where the outer layer is precipitated in close association with photosymbiont-bearing siphonal mantle, and the inner layer is grown in association with the light-starved inner mantle. We collected 38 shells of the three species (the cosmopolitan Tridacna maxima and T. squamosa, as well as the rare endemic T. squamosina),...

Understanding forest dynamics by integrating age and environmental change

Kai Zhu
How much carbon a forest ecosystem can sequester is determined by both post-disturbance regrowth and environmentally modified growth. Disturbance causes sharp declines in the short term and is followed by regrowth in the long term. Environmental change may alter carbon accumulation through increasing CO2, nitrogen deposition, and climate change. Regrowth and modified growth occur simultaneously, yet they are usually studied separately and assessed using an additive approach. Alternatively, an interactive approach using hierarchical models can...

How climate impacts the composition of wolf killed-elk in northern Yellowstone National Park

Christopher Wilmers, Matthew Metz, Daniel Stahler, Michel Kohl, Chris Geremia & Douglas Smith
1. While the functional response of predators is commonly measured, recent work has revealed that the age and sex composition of prey killed is often a better predictor of prey population dynamics because the reproductive value of adult females is usually higher than that of males or juveniles. 2. Climate is often an important mediating factor in determining the composition of predator kills, but we currently lack a mechanistic understanding of how the multiple facets...

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...

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...

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...

Forest Survey data 2012-2013

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

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...

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.

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: 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: 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...

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...

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...

The WeAllWalk Data Set

German Flores & Roberto Manduchi
This data set contains time series from inertial sensors carried by blind subjects walking through pre-determined routes In two buildings in the UCSC campus. The sensors include two MetaWear CPRO (obtaining a tri-axial accelerometer and gyroscope) and two iPhone 6 containing try-axial accelerometer, gyroscopes, and magnetometers. This data set is described in the paper: Flores, German, and Roberto Manduchi. "WeAllWalk: An Annotated Data Set of Inertial Sensor Time Series from Blind Walkers", Proceedings of the...

UVS Occultation Altimetry Code and Synthetic Data

Jacob Abrahams
This contains the code used to produce the figures in our UVS Occultation Altimetry manuscript, as well as the observation locations and synthetic data required to run the code. There are 9 .txt files, one is our nominal shape model, one is the set of chord ingress and egress points, three of them contain the locations of radar altimetric measurements for different truncation altitudes, and four of them contain precomputed lengths corresponding to our nominal...

Pluto and Charon limb profile topography

Jack Conrad
We derived updated and expanded topography datasets for Pluto and Charon. This is done through finding the body edge (i.e. the limb) in images, and with those body edge locations we can apply simple geographical techniques to produce limb profiles. The process involves some human intervention, but is primarily automation based. Our limb profile topography is useful for geologic and geophysical studies of Pluto and Charon. Additionally, we provide processed data of how we used...

Runoff modeling of a coastal basin to assess variations in response to shifting climate and land use: Implications for managed recharge

Sarah Beganskas, Kyle Young, Andrew Fisher, Ryan Harmon & Sacha Lozano
We quantified hillslope runoff distribution in a coastal, mixed-use basin, the Pajaro Valley Drainage Basin (PVDB), under different climate and land use conditions, evaluating the potential for distributed stormwater collection coupled with managed aquifer recharge (DSC-MAR) to improve groundwater supply. We developed dry, normal, and wet climate scenarios using historic precipitation and temperature data, and we compared contemporary land use to pre-development land use by replacing developed areas in the model with plausible native vegetation...

Chemical shift-based methods in NMR structure determination

Santrupti Nerli, Andrew C. McShan & Nikolaos G. Sgourakis
Chemical shifts are highly sensitive probes that can be harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary automated and computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high-resolution protein and nucleic...

Fractional crystallization of a Martian magma ocean and formation of a thermochemical boundary layer at the base of the mantle

Garrett Zeff
BurnMan and pMELTS outputs for simulations of fractionally crystallizing magma oceans on Mars.

Natural enemy-herbivore networks along local management and landscape gradients in urban agroecosystems

Stacy Philpott, Azucena Lucatero, Peter Bichier, Monika Egerer, Shalene Jha, Brenda Lin & Heidi Liere
Ecological networks can provide insight into how biodiversity loss and changes in species interactions impact the delivery of ecosystem services. In agroecosystems that vary in management practices, quantifying changes in ecological network structure across gradients of local and landscape composition can inform both the ecology and function of productive agroecosystems. In this study, we examined natural enemy-herbivore co-occurrence networks associated with Brassica oleracea (cole crops), a common crop in urban agricultural systems. Specifically, we investigated...

Año Nuevo Island Animal Count: analyzing citizen science pinniped counts from drone imagery

Sarah Wood
Fluctuations in marine mammal abundance can reveal changes in local ecosystem health and inform conservation strategies. Unmanned aircraft systems (UAS) such as drones are increasingly being used to photograph and count marine mammals in remote locations; however, counting animals in images is a laborious task. Crowd-sourced science has the potential to considerably reduce the time required to conduct these censuses but must first be validated against expert counts to confirm accuracy. Our objectives were to...

Isotopic evidence for long-distance connections of the AD thirteenth century Promontory caves occupants

Jessica Metcalfe, John Ives, Sabrina Shirazi, Kevin Gilmore, Jennifer Hallson, Fiona Brock, Bonnie Clark & Beth Shapiro
The Promontory caves (Utah) and Franktown Cave (Colorado) contain high-fidelity records of short-term occupations by groups with material culture connections to the Subarctic/Northern Plains. This research uses Promontory and Franktown bison dung, hair, hide, and bone collagen to establish local baseline carbon isotopic variability and identify leather from a distant source. The ankle wrap of one Promontory Cave 1 moccasin had a δ13C value that indicates a substantial C4 component to the animal’s diet, unlike...

Registration Year

  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016

Resource Types

  • Dataset
  • Collection


  • University of California, Santa Cruz
  • Organization For Tropical Studies
  • Organization for Tropical Studies
  • Missouri Botanical Garden
  • The University of Texas at Austin
  • University of Alberta
  • University of San Francisco
  • Seattle University
  • Virginia Tech
  • University of Costa Rica