19 Works

Data from: Implications of survey effort on estimating demographic parameters of a long-lived marine top predator

John Symons, Kate R. Sprogis & Lars Bejder
Effective management of wildlife populations rely on knowledge of their abundance, survival and reproductive rates. Maintaining long-term studies capable of estimating demographic parameters for long-lived, slow reproducing species is challenging. Insights into effects of research intensity on the statistical power to estimate demographic parameters is limited. Here, we investigate implications of survey effort on estimating abundance, home range sizes and reproductive output of Indo-Pacific bottlenose dolphins (Tursiops aduncus), using a three-year sub-sample of a long-term,...

Data from: The ephemerality of secondary forests in southern Costa Rica

J. Leighton Reid, Matthew E. Fagan, James Lucas, Joshua Slaughter & Rakan A. Zahawi
Secondary forests are increasingly recognized for conserving biodiversity and mitigating global climate change, but these and other desired outcomes can only be achieved after decades of regeneration, and secondary forests are frequently recleared before they recover to predisturbance conditions. We used a time series of aerial photographs (1947-2014) to evaluate multidecadal persistence of secondary forests across a 320 sq. km landscape in southern Costa Rica. Secondary forests had relatively short lifespans, with 50% recleared within...

Data from: Transpacific coalescent pathways of coconut rhinoceros beetle biotypes: resistance to biological control catalyzes resurgence of an old pest

Jonathan Bradley Reil, Camiel Doorenweerd, Michael San Jose, Sheina B. Sim, Scott M. Geib & Daniel Rubinoff
Biological control agents have several advantages over chemical control for pest management, including the capability to restore ecosystem balance with minimal non-target effects and a lower propensity for targets to develop resistance. These factors are particularly important in the invasive species control. The coconut rhinoceros beetle (Oryctes rhinoceros Linnaeus) is a major palm pest that invaded many Pacific islands in the early 20th century through human-mediated dispersal. Application of the Oryctes nudivirus in the 1960’s...

Data from: Combining fish and benthic communities into multiple regimes reveals complex reef dynamics

Mary K. Donovan, Alan M. Friedlander, Joey Lecky, Jean-Baptiste Jouffray, Gareth J. Williams, Lisa M. Wedding, Larry B. Crowder, Ashley L. Erickson, Nick A. J. Graham, Jamison M. Gove, Carrie V. Kappel, Kendra Karr, John N. Kittinger, Albert V. Norström, Magnus Nyström, Kirsten L. L. Oleson, Kostantinos A. Stamoulis, Crow White, Ivor D. Williams & Kimberly A. Selkoe
Coral reefs worldwide face an uncertain future with many reefs reported to transition from being dominated by corals to macroalgae. However, given the complexity and diversity of the ecosystem, research on how regimes vary spatially and temporally is needed. Reef regimes are most often characterised by their benthic components; however, complex dynamics are associated with losses and gains in both fish and benthic assemblages. To capture this complexity, we synthesised 3,345 surveys from Hawai‘i to...

Data from: Phylogenomics supports incongruence between ecological specialization and taxonomy in a charismatic clade of buck moths

Julian R. Dupuis, Richard S. Peigler, Scott M. Geib & Daniel Rubinoff
Local adaptation can be a fundamental component of speciation, but its dynamics in relation to gene flow are not necessarily straightforward. Herbivorous taxa with localized host plant or habitat specialization across their geographic range are ideal models for investigating the patterns and constraints of local adaptation and its impact on diversification. The charismatic, day-flying moths of the Hemileuca maia species complex (Lepidoptera: Saturniidae) are such taxa, as they are geographically-widespread, exhibit considerable ecological and morphological...

Data from: Would an RRS by any other name sound as RAD?

Erin O. Campbell, Bryan M.T. Brunet, Julian R. Dupuis, Felix A.H. Sperling, Bryan M. T. Brunet & Felix A. H. Sperling
1. Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as restriction site-associated DNA sequencing (RADseq). But naming conventions have often been more creative than consistent and criteria for recognizing unique methods have been unclear, resulting in a proliferation of names characterized by ambiguity. 2. We...

Data from: The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions

Jeremy M. Brown & Robert C. Thomson
Bayesian phylogenetic inference involves sampling from posterior distributions of trees, which sometimes exhibit local optima, or peaks, separated by regions of low posterior density. Markov chain Monte Carlo (MCMC) algorithms are the most widely used numerical method for generating samples from these posterior distributions, but they are susceptible to entrapment on individual optima in rugged distributions when they are unable to easily cross through or jump across regions of low posterior density. Ruggedness of posterior...

Data from: Nutrient pollution disrupts key ecosystem functions on coral reefs

Nyssa J. Silbiger, Craig E. Nelson, Kristina Remple, Jessica K. Sevilla, Zachary A. Quinlan, Hollie M. Putnam, Michael D. Fox & Megan J. Donahue
There is a long history of examining the impacts of nutrient pollution and pH on coral reefs. However, little is known about how these two stressors interact and influence coral reef ecosystem functioning. Using a six-week nutrient addition experiment, we measured the impact of elevated nitrate (NO3) and phosphate (PO43) on net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities. Our study had four major outcomes: 1)...

Data from: Genomewide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

Nathan Taitano, Vivian Bernau, Lev Jardón-Barbolla, Brian Leckie, Michael Mazourek, Kristin Mercer, Leah McHale, Andrew Michel, David Baumler, Michael Kantar, Esther Van Der Knapp & Esther Van Der Knaap
Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping-by-sequencing (GBS), yielding 32,623 filtered...

Data from: Invasive rat eradication strongly impacts plant recruitment on a tropical atoll

Coral A. Wolf, Hillary S. Young, Kelly M. Zilliacus, Alex S. Wegmann, Matthew McKown, Nick D. Holmes, Bernie R. Tershy, Rodolfo Dirzo, Stefan Kropidlowski, Donald A. Croll & Alexander S. Wegmann
Rat eradication has become a common conservation intervention in island ecosystems and its effectiveness in protecting native vertebrates is increasingly well documented. Yet, the impacts of rat eradication on plant communities remain poorly understood. Here we compare native and non-native tree and palm seedling abundance before and after eradication of invasive rats (Rattus rattus) from Palmyra Atoll, Line Islands, Central Pacific Ocean. Overall, seedling recruitment increased for five of the six native trees species examined....

Data from: An extensive suite of functional traits distinguishes wet and dry Hawaiian forests and enables prediction of species vital rates

Camila D. Medeiros, Christine Scoffoni, Grace John, Megan Bartlett, Faith Inman-Narahari, Rebecca Ostertag, Susan Cordell, Christian Giardina, Lawren Sack, Megan K. Bartlett & Grace P. John
1. The application of functional traits to predict and explain plant species’ distributions and vital rates has been a major direction in functional ecology for decades, yet numerous physiological traits have not yet been incorporated into the approach. 2. Using commonly measured traits such as leaf mass per area (LMA) and wood density (WD), and additional traits related to water transport, gas exchange and resource economics, including leaf vein, stomatal, and wilting traits, we tested...

Data from: Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?

Emilie J. Richards, Jeremy M. Brown, Anthony J. Barley, Rebecca A. Chong & Robert C. Thomson
The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation,...

Data from: Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

Christopher E. Laumer, Harald Gruber-Vodicka, Michael G. Hadfield, Vicki B. Pearse, Ana Riesgo, John C. Marioni & Gonzalo Giribet
The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for...

Data from: Persistence at the final stage of volcanic island ontogeny: abiotic predictors explain native plant species richness on 111 remote Pacific atolls

Sebastien Larrue, Jean-François Butaud, Curtis C. Daehler, Stéphane Ballet, Julien Chadeyron & Roger Oyono
Aim: The final island ontogeny of the General Dynamic Model (GDM) (i.e. before island submergence) in tropical oceans corresponds to the coral atoll stage. Here, we examined whether the species richness of native vascular plants (indigenous and endemic species) on atolls is controlled by spatial and/or physical processes. We also predicted that atolls strongly affected by anthropogenic disturbance would have lower native species richness than predicted by spatial and physical processes. Location: Marshall Islands, Kiribati...

Data from: Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation

Levi N. Gray, Anthony J. Barley, Steven Poe, Robert C. Thomson, Adrián Nieto-Montes De Oca & Ian J. Wang
A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history, and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions, and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially...

Data from: Elemental content and stoichiometry of SAR11 chemoheterotrophic marine bacteria

Angelicque E. White, Stephen J. Giovannoni, Yanlin Zhao, Kevin Vergin & Craig A. Carlson
We measured the carbon, nitrogen, and phosphorus content and production of cultured SAR11 cells in the genus Pelagibacter, from members of the 1a.1 and 1a.3 lineages, which are adapted to productive coastal waters and oligotrophic tropical/subtropical environments, respectively. The average growing SAR11 cell contained ~6.5 fg C, from which we calculated a global standing stock of 1.4 1013 g C. Calculations that consider uncertainties in cell turnover rates and growth efficiencies indicate this stock could...

Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing

Julian R. Dupuis, Forest T. Bremer, Angela Kauwe, Michael San Jose, Luc Leblanc, Daniel Rubinoff & Scott M. Geib
High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive...

Data from: Flickers of speciation? Sympatric color morphs of the arc-eye hawkfish, Paracirrhites arcatus, reveal key elements of divergence-with-gene-flow

Jonathan L. Whitney, Brian W. Bowen & Stephen A. Karl
One of the primary challenges of evolutionary research is to identify ecological factors that favor reproductive isolation. Therefore, studying partially isolated taxa has the potential to provide novel insight into the mechanisms of evolutionary divergence. Our study utilizes an adaptive color polymorphism in the arc-eye hawkfish (Paracirrhites arcatus) to explore the evolution of reproductive barriers in the absence of geographic isolation. Dark and light morphs are ecologically partitioned into basaltic and coral microhabitats a few...

Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])

Michael San Jose, Camiel Doorenweerd, Luc Leblanc, Norman Barr, Scott Geib & Daniel Rubinoff
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Hawaii at Manoa
  • United States Department of Agriculture
  • Stanford University
  • University of California System
  • National Autonomous University of Mexico
  • University of California, Santa Barbara
  • University of Idaho
  • Louisiana State University of Alexandria
  • California State University, Northridge
  • Bangor University