119 Works

Data from: Large-scale introduction of the Indo-Pacific damselfish Abudefduf viagiensis into Hawai‘i promotes genetic swamping of the endemic congener A. abdominalis

Richard R. Coleman, Michelle R. Gaither, Kimokeo Bethany, Stanton Frank, Brian W. Bowen, Robert J. Toonen & Bethany Kimokeo
Hybridization in the ocean was once considered rare, a process prohibited by the rapid evolution of intrinsic reproductive barriers in a high-dispersal medium. However, recent genetic surveys have prompted a reappraisal of marine hybridization as an important demographic and evolutionary process. The Hawaiian Archipelago offers an unusual case history in this arena, due to the recent arrival of the widely distributed Indo-Pacific Sergeant (Abudefduf vaigiensis), which is hybridizing with the endemic congener, A. abdominals. Surveys...

Data from: Assessing the performance of DNA barcoding using posterior predictive simulations

Anthony J. Barley & Robert C. Thomson
Accurate estimates of biodiversity are required for research in a broad array of biological subdisciplines including ecology, evolution, systematics, conservation and biodiversity science. The use of statistical models and genetic data, particularly DNA barcoding, has been suggested as an important tool for remedying the large gaps in our current understanding of biodiversity. However, the reliability of biodiversity estimates obtained using these approaches depends on how well the statistical models that are used describe the evolutionary...

Data from: When environmental factors become stressors: interactive effects of vermetid gastropods and sedimentation on corals

Julie Zill, Michael A. Gil, Craig W. Osenberg & Julie A. Zill
Environmental stressors often interact, but most studies of multiple stressors have focused on combinations of abiotic stressors. Here we examined the potential interaction between a biotic stressor, the vermetid snail Ceraesignum maximum, and an abiotic stressor, high sedimentation, on the growth of reef-building corals. In a field experiment, we subjected juvenile massive Porites corals to four treatments: (i) neither stressor, (ii) sedimentation, (iii) vermetids or (iv) both stressors. Unexpectedly, we found no effect of either...

Data from: Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association

Sarah E. Kingston, Pieter Martino, Marko Melendy, Floyd A. Reed & David B. Carlon
A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification...

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: Impact of model violations on the inference of species boundaries under the multispecies coalescent

Anthony J. Barley, Jeremy M. Brown & Robert C. Thomson
The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence, and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning...

Data from: The relationship between microhabitat use, allometry, and functional variation in the eyes of Hawaiian Megalagrion damselflies

Jeffrey A. Scales & Marguerite A. Butler
The evolution of visual systems is guided by visual requirements imposed by the environment, the size of the animal's eyes, and physical limitations imposed by the resolution-sensitivity trade-off. Given a particular eye surface area, resolution and sensitivity cannot be simultaneously maximized: gains in resolution, the ability of the eye to detect detail, will come at the cost of sensitivity, the ability to capture photons, and vice versa, without an increase to eye size. How this...

Data from: Can the source-sink hypothesis explain macrofaunal abundance patterns in the abyss? A modeling test

Sarah M. Hardy, Craig R. Smith & Andreas M. Thurnherr
Low food availability is a major structuring force in deep-sea benthic communities, sustaining only very low densities of organisms in parts of the abyss. These low population densities may result in an Allee effect, whereby local reproductive success is inhibited, and populations are maintained by larval dispersal from bathyal slopes. This slope–abyss source–sink (SASS) hypothesis suggests that the abyssal seafloor constitutes a vast sink habitat with macrofaunal populations sustained only by an influx of larval...

Data from: Adaptive responses and local stressor mitigation drive coral resilience in warmer, more acidic oceans

Christopher P. Jury & Robert J. Toonen
Coral reefs have great biological and socioeconomic value, but are threatened by ocean acidification, climate change, and local human impacts. The capacity for corals to adapt or acclimatise to novel environmental conditions is unknown but fundamental to projected reef futures. The coral reefs of Kāne‘ohe Bay, Hawai‘i were devastated by anthropogenic insults from the 1930s-1970s. These reefs experience naturally reduced pH and elevated temperature relative to many other Hawaiian reefs which are not expected to...

Data from: Developmental constraints and resource environment shape early emergence and investment in spines in saplings

Mohammed Armani, Tristan Charles-Dominique, Kasey E. Barton & Kyle W. Tomlinson
Abstract Background and Aims Herbivory by large mammals imposes a critical recruitment bottleneck on plants in many systems. Spines defend plants against large herbivores and how early they emerge in saplings may be one of the strongest predictors of sapling survival in herbivore-rich environments. Yet little effort has been directed at understanding the variability in spine emergence across saplings. Methods We present a multi-species study examining whether and how sapling size,spine type and species’ environmental...

Data from: Going with the flow: hydrodynamic cues trigger directed escapes from a stalking predator

Lillian J. Tuttle, H. Eve Robinson, Daisuke Takagi, J. Rudi Strickler, Petra H. Lenz & Daniel K. Hartline
In the coevolution of predator and prey, different and less well understood rules for threat-assessment apply to freely suspended organisms than to substrate-dwelling ones. Particularly vulnerable are small prey carried with the bulk movement of a surrounding fluid and thus deprived of sensory information within the bow waves of approaching predators. Some planktonic prey have solved this apparent problem, however. We quantified cues generated by the slow approach of larval clownfish (Amphiprion ocellaris) that triggered...

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...

Best-practice forestry management delivers diminishing returns for coral reefs with increased land-clearing

Amelia Wenger, Daniel Harris, Samuel Weber, Ferguson Vaghi, Yashika Nand, Waisea Naisilisili, Alec Hughes, Jade Delevaux, Carissa Klein, James Watson, Peter Mumby & Stacy Jupiter
Protection of coastal ecosystems from deforestation may be the best way to protect coral reefs from sediment runoff. However, given the importance of generating economic activities for coastal livelihoods, the prohibition of development is often not feasible. In light of this, logging codes-of-practice have been developed to mitigate the impacts of logging on downstream ecosystems. However, no studies have assessed whether managed land-clearing can occur in tandem with coral reef conservation goals. This study quantifies...

Stacking microscopy images of the pteropod Limacina bulimoides

Le Qin Choo, Thijs M. P. Bal, Erica Goetze & Katja T. C. A. Peijnenburg
Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large scale population structuring of...

Additive and non-additive responses of seedlings to simulated herbivory and drought data

Kasey Barton & Aaron Shiels
Drought is a global threat, increasing in severity and frequency throughout tropical ecosystems. Although plants often face drought in conjunction with biotic stressors, such as herbivory or disease, experimental studies infrequently test the simultaneous effects of drought and biotic stress. Because multiple simultaneous stressors may have non-additive and complex effects on plant performance, it is difficult to predict plant responses to multiple threats from research examining one stress at a time. Using an experimental approach...

Fungal infection alters the selection, dispersal, and drift processes structuring the amphibian skin microbiome

Mark Q Wilber, Andrea J Jani, Joseph R Mihaljevic & Cheryl J Briggs
Symbiotic microbial communities are important for host health, but the processes shaping these communities are poorly understood. Understanding how community assembly processes jointly affect microbial community composition is limited because inflexible community models rely on rejecting dispersal and drift before considering selection. We developed a flexible community assembly model based on neutral theory to ask: How do dispersal, drift, and selection concurrently affect the microbiome across environmental gradients? We applied this approach to examine how...

Human impact, climate and dispersal strategies determine plant invasion on islands

Severin D. H. Irl, Andreas H. Schweiger, Manuel J. Steinbauer, Claudine Ah-Peng, José R. Arévalo, Carl Beierkuhnlein, Alessandro Chiarucci, Curtis C. Daehler, José M. Fernández-Palacios, Olivier Flores, Christoph Kueffer, Petr Madera, Rüdiger Otto, Julienne M. I. Schweiger, Dominique Strasberg & Anke Jentsch
Aim: Biological invasions are likely determined by species dispersal strategies as well as environmental characteristics of a recipient region, especially climate and human impact. However, the contribution of climatic factors, human impact and dispersal strategies in driving invasion processes is still controversial and not well embedded in the existing theoretical considerations. Here, we study how climate, species dispersal strategies and human impact determine plant invasion processes on islands distributed in all major oceans in the...

The Depiction of Japanese Homosexuality through Masks and Mirrors

Thomas Schmidt
Matsumoto Toshio’s avant-garde documentary Funeral Parade of Roses (bara no sōretsu) depicts life in Shinjuku’s 1960s underground culture. Using Sakabe Megumi’s hermeneutical theory, the film’s depiction of sexuality is analysed through its use of literal and figurative mirrors and masks. It is argued that sexuality is highly performative and that the film itself is structured like a play of mirrors, questioning the nature of reality by deferring hypostasis ad infinitum. Keywords: Sakabe Megumi, Mirror and...

Data from: Rapid scavenging of jellyfish carcasses reveals the importance of gelatinous material to deep-sea food webs

Andrew K. Sweetman, Craig R. Smith, Trine Dale & Daniel O. B. Jones
Jellyfish blooms are common in many oceans, and anthropogenic changes appear to have increased their magnitude in some regions. Although mass falls of jellyfish carcasses have been observed recently at the deep seafloor, the dense necrophage aggregations and rapid consumption rates typical for vertebrate carrion have not been documented. This has led to a paradigm of limited energy transfer to higher trophic levels at jelly falls relative to vertebrate organic falls. We show from baited...

Data from: Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral, Pocillopora damicornis

Kelvin D. Gorospe & Stephen A. Karl
Patterns of isolation-by-distance are uncommon in coral populations. Here, we depart from historical trends of large-scale, geographic genetic analyses by scaling down to a single patch reef in Kāne‘ohe Bay, Hawai‘i, and map and genotype all colonies of the coral, Pocillopora damicornis. Six polymorphic microsatellite loci were used to assess population genetic and clonal structure and to calculate individual colony pairwise relatedness values. Our results point to an inbred, highly clonal reef (between 53 and...

Data from: Adaptive morphological shifts to novel habitats in marine sculpin fishes

Matthew L. Knope & Jeffrey A. Scales
Sculpin fishes of the North American Pacific Coast provide an ideal opportunity to examine whether adaptive morphological character shifts have facilitated occupation of novel habitat types because of their well-described phylogeny and ecology. In this group, the basal-rooted species primarily occupy the subtidal habitat, whereas the species in the most distal clades are found in the intertidal. We tested multiple evolutionary models to determine whether changes in body size and changes in number of scales...

Evaluation of Electronic Monitoring Pre-implementation in the Hawaiʻi-based Longline Fisheries

Matthew J. Carnes, Jennifer Paige Stahl & Keith A. Bigelow
NOAA technical memorandum NMFS-PIFSC ; 90

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...

Spatial drivers of composition and connectivity across endangered tropical dry forests

Chris Balzotti, Gregory Asner, Edith Adkins & Elliott Parsons
1. Tropical dry forests are among the most threatened ecosystems in the world. Rapid loss, degradation, and fragmentation of these native ecosystems in a changing climate have driven a time-sensitive need to improve our understanding and management of remaining dry forests. 2. We used advanced remote sensing technologies, combined with extensive field data and machine learning, to better understand how spatial drivers (e.g., climate, fire, human) of canopy species composition vary in importance and correlate...

Data from: Properties of Markov chain Monte Carlo performance across many empirical alignments -- part I

Sean M Harrington, Van Wishingrad & Robert C Thomson
Nearly all current Bayesian phylogenetic applications rely on Markov chain Monte Carlo (MCMC) methods to approximate the posterior distribution for trees and other parameters of the model. These approximations are only reliable if Markov chains adequately converge and sample from the joint posterior distribution. While several studies of phylogenetic MCMC convergence exist, these have focused on simulated datasets or select empirical examples. Therefore, much that is considered common knowledge about MCMC in empirical systems derives...

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