214 Works

Data from: Distinct predatory behaviors in scimitar- and dirk-toothed sabertooth cats

Borja Figueirido, Stephan Lautenschlager, Alejandro Perez-Ramos & Blaire Van Valkenburgh
Over the Cenozoic, large cat-like forms have convergently evolved into specialized killers of ‘megaherbivores’ that relied on their large, and laterally-compressed (saber-like) canines to rapidly subdue their prey [1-5]. Scimitar- and dirk-toothed sabertooths are distinct ecomorphs that differ in canine tooth length, degree of serration, and postcranial features indicative of dissimilar predatory behavior [6-13]. Despite these differences, it is assumed that they used a similar ‘canine-shear’ bite to kill their prey [14,15]. We investigated the...

Data from: A comparison of genomic islands of differentiation across three young avian species pairs

Darren E. Irwin, Borja Milá, David P. L. Toews, Alan Brelsford, Haley L. Kenyon, Alison N. Porter, Christine Grossen, Kira E. Delmore, Miguel Alcaide & Jessica H. Irwin
Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., “islands of differentiation” in FST), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's / mourning...

Data from: Integrating vital rates explains optimal worker size for resource return by bumble bee workers

Natalie Z. Kerr, Elizabeth E. Crone & Neal M. Williams
1. Size-number trade-offs in reproduction are commonly observed in nature. Bumble bee (Bombus spp.) colonies produce workers that vary considerably in size. This variation suggests that colonies face potential size-number trade-offs when producing workers. 2. Here, we estimated size-based vital rates of Bombus vosnesenskii workers using colonies reared from wild caught queens. We conducted a mark-recapture study to estimate worker survival as a function of body size. We also collected data on pollen and nectar...

Data from: Temporal structure of human gaze dynamics is invariant during free viewing

Colleen A. Marlow, Indre V. Viskontas, Alisa Matlin, Cooper Boydston, Adam Boxer & Richard P. Taylor
We investigate the dynamic structure of human gaze and present an experimental study of the frequency components of the change in gaze position over time during free viewing of computer-generated fractal images. We show that changes in gaze position are scale-invariant in time with statistical properties that are characteristic of a random walk process. We quantify and track changes in the temporal structure using a well-defined scaling parameter called the Hurst exponent, H. We find...

Data from: Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation

Oscar Beijbom, Peter J. Edmunds, Chris Roelfsema, Jennifer Smith, David I. Kline, Benjamin Neal, Matthew J. Dunlap, Vincent Moriarty, Tung-Yung Fan, Chih-Jui Tan, Stephen Chan, Tali Treibitz, Anthony Gamst, B. Greg Mitchell, David Kriegman & Benjamin P. Neal
Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and...

Data from: Socially selected ornaments and fitness: signals of fighting ability in paper wasps are positively associated with survival, reproductive success, and rank

Elizabeth Alison Tibbetts, Taylor Forrest, Cassondra Vernier, Judy Jinn & Andrew Madagame
Many animals have ornaments that mediate choice and competition in social and sexual contexts. Individuals with elaborate sexual ornaments typically have higher fitness than those with less elaborate ornaments, but less is known about whether socially selected ornaments are associated with fitness. Here, we test the relationship between fitness and facial patterns that are a socially-selected signal of fighting ability in Polistes dominula wasps. We found wasps that signal higher fighting ability have larger nests,...

Data from: The relationship between risk of bias criteria, research outcomes, and study sponsorship in a cohort of preclinical thiazolidinedione animal studies: a meta-analysis

Maher Abdel-Sattar, David Krauth, Andrew Anglemyer & Lisa Bero
Introduction: There is little evidence regarding the influence of conflicts of interest on preclinical research. This study examines whether industry sponsorship is associated with increased risks of bias and/or effect sizes of outcomes in published preclinical thiazolidinedione (TZD) studies. Methods: We identified preclinical TZD studies published between January 1, 1965, and November 14, 2012. Coders independently extracted information on study design criteria aimed at reducing bias, results for all relevant outcomes, sponsorship source and investigator...

Data from: Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient

Nicholas J. Kooyers, Brooke James & Benjamin K. Blackman
Closely related species may evolve to coexist stably in sympatry through niche differentiation driven by in situ competition, a process termed character displacement. Alternatively, past evolution in allopatry may have already sufficiently reduced niche overlap to permit establishment in sympatry, a process called ecological sorting. The relative importance of each process to niche differentiation is contentious even though they are not mutually exclusive and are both mediated via multivariate trait evolution. We explore how competition...

Data from: The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

Henrik Krehenwinkel, Marisa Fong, Susan Kennedy, Edward Greg Huang, Suzuki Noriyuki, Luis Cayetano & Rosemary Gillespie
PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias...

Data from: Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

Nicolas J. Rawlence, Martyn Kennedy, Christian N. K. Anderson, Stefan Prost, Charlotte E. Till, Ian Smith, R. Paul Scofield, Alan J. D. Tennyson, Jill Hamel, Chris Lalas, Elizabeth A. Matisoo-Smith, Jonathan M. Waters & Ian W. G. Smith
Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the...

Data from: Elevating perceived predation risk modifies the relationship between parental effort and song complexity in the song sparrow (Melospiza melodia)

Melissa L. Grunst, John T. Rotenberry & Andrea S. Grunst
Adult-directed predation risk elevates costs of parental care, and may modify relationships between sexually selected ornaments and parental effort by accentuating the tradeoff between survival and parental investment. We assessed multiple hypotheses regarding the relationship between maternal effort, paternal effort, and the sexually selected trait of male song complexity in the song sparrow Melospiza melodia. Further, we explored whether experimentally elevating perceived adult-directed predation risk near nests affected these relationships. We quantified two dimensions of...

Data from: Post-fire recovery in coastal sage scrub: seed rain and community trajectory

Erin Conlisk, Rebecca Swab, Alejandra Martínez-Berdeja & Matthew P. Daugherty
Disturbance is a primary mechanism structuring ecological communities. However, human activity has the potential to alter the frequency and intensity of natural disturbance regimes, with subsequent effects on ecosystem processes. In Southern California, human development has led to increased fire frequency close to urban areas that can form a positive feedback with invasive plant spread. Understanding how abiotic and biotic factors structure post-fire plant communities is a critical component of post-fire management and restoration. In...

Data from: Sex-biased transcriptomic response of the reproductive axis to stress

Rebecca M. Calisi, Suzanne H. Austin, Andrew S. Lang & Matthew D. MacManes
Stress is a well-known cause of reproductive dysfunction in many species, including birds, rodents, and humans, though males and females may respond differently. A powerful way to investigate how stress affects re- production is by examining its effects on a biological system essential for regulating reproduction, the hy- pothalamic-pituitary-gonadal (HPG) axis. Often this is done by observing how a stressor affects the amount of glucocorticoids, such as cortisol or corticosterone, circulating in the blood and...

Data from: A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna

Henrik Krehenwinkel, Maxene Graze, Dennis Roedder, Tanaka Kazuhiro, Yuki G. Baba, Christoph Muster, Gabriele Uhl & Kazuhiro Tanaka
Aim: The phylogeographical history of wide-ranging Palaearctic species is not well understood. Here, we present a range-wide phylogeographical study of the wasp spider, Argiope bruennichi (Scopoli, 1772), a highly dispersive and widely distributed Palaearctic species. We aim to identify glacial refugia and patterns of interglacial gene flow across the Palaearctic. Location: Palaearctic region, including the Azores, Madeira, Europe, North Africa and Asia. Methods: We conduct a range-wide phylogeographical survey. Our study is based on nuclear...

Data from: Genetic basis of between-individual and within-individual variance of docility

Julien G.A. Martin, Enrico Pirottay, Matthew B. Petellez, Daniel T. Blumstein, J. G. A. Martin, E. Pirotta & M. B. Petelle
Between-individual variation in phenotypes within a population is the basis of evolution. However, evolutionary and behavioural ecologists have mainly focused on estimating between-individual variance in mean trait and neglected variation in within-individual variance, or predictability of a trait. In fact, an important assumption of mixed-effects models used to estimate between-individual variance in mean traits is that within-individual residual variance (predictability) is identical across individuals. Individual heterogeneity in the predictability of behaviours is a potentially important...

Data from: Herbivore size matters for productivity-richness relationships in African savannas

Deron E. Burkepile, Richard W. S. Fynn, Dave I. Thompson, Nathan P. Lemoine, Sally E. Koerner, Stephanie Eby, Nicole Hagenah, Kevin R. Wilcox, Scott L. Collins, Kevin P. Kirkman, Alan K. Knapp & Melinda D. Smith
1.Productivity and herbivory often interact to shape plant community composition and species richness with levels of production mediating the impact of herbivory. Yet, differences in herbivore traits such as size, feeding guild, and dietary requirements may result in different impacts of diverse herbivore guilds across productivity gradients. 2.We used size-selective herbivore exclosures to separate the effects of herbivory by larger herbivores, such as elephant, Burchell's zebra, and blue wildebeest from those of medium/smaller herbivores, such...

Data from: Engineering ER-stress dependent non-conventional mRNA splicing

Weihan Li, Voytek Okreglak, Jirka Peschek, Philipp Kimmig, Meghan Zubradt, Jonathan S. Weissman & Peter Walter
The endoplasmic reticulum (ER) protein folding capacity is balanced with the protein folding burden to prevent accumulation of un- or misfolded proteins. The ER membrane-resident kinase/RNase Ire1 maintains ER protein homeostasis through two fundamentally distinct processes. First, Ire1 can initiate a transcriptional response through a non-conventional mRNA splicing reaction to increase the ER folding capacity. Second, Ire1 can decrease the ER folding burden through selective mRNA decay. In Saccharomyces cerevisiae and Schizosaccharomyces pombe, the two...

Data from: Genetic structure of the Painted Bunting and its implications for conservation of migratory populations

Andrea Contina, Jose L. Alcantara, Eli S. Bridge, Jeremy D. Ross, Oakley F. William, Jeffrey F. Kelly, Kristen C. Ruegg & William F. Oakley
The Painted Bunting Passerina ciris is a Neotropical songbird which breeds primarily in the United States during the summer and migrates to Mexico, Central America, southern Florida, and the Caribbean over the winter. Male Painted Buntings are brightly coloured, which makes them highly sought after as pets, particularly in Mexico, Central America and Europe. We used short sequence repeats (microsatellite DNA) to investigate the population genetic structure of the Painted Bunting and its implications in...

Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

Michael J. Landis, William A. Freyman & Bruce G. Baldwin
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. Without fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the...

Data from: Phenology and the physiological niche are co-adapted in a desert dwelling lizard

Bao-Jun Sun, Liang Ma, Shu-Ran Li, Caroline M. Williams, Yang Wang, Xin Hao & Wei-Guo Du
1. A major goal of seasonal biology is to understand how selection on phenology and the physiological niche interact. In oviparous species, fitness variation across the growing season suggests that phenological shifts will alter selective environments experienced by embryos. We hypothesize that physiology could become co-adapted with phenology; such that embryos perform better in the environmental conditions they are adapted to compared to embryos adapted to other environments (temporal matching). 2. Here, we tested for...

Data from: Forest disturbance accelerates thermophilization of understory plant communities

Jens T. Stevens, Hugh D. Safford, Susan Harrison & Andrew M. Latimer
1. Climate change is likely to shift plant communities towards species from warmer regions, a process termed “thermophilization.” In forests, canopy disturbances such as fire may hasten this process by increasing temperature and moisture stress in the understory, yet little is known about the mechanisms that might drive such shifts, or the consequences of these processes for plant diversity. 2. We sampled understory vegetation across a gradient of disturbance severity from a large-scale natural experiment...

Data from: Seasonal variation in daily patterns of social contacts in the European badger Meles meles

Matthew J. Silk, Nicola Weber, Lucy C. Steward, Richard J. Delahay, Darren P. Croft, David J. Hodgson, Mike Boots & Robbie A. McDonald
Social interactions among hosts influence the persistence and spread of infectious pathogens. Daily and seasonal variation in the frequency and type of social interactions will play an important role in disease epidemiology and, alongside other factors, may have an influence on wider disease dynamics by causing seasonal forcing of infection, especially if the seasonal variation experienced by a population is considerable. We explored temporal variation in within-group contacts in a high-density population of European badgers...

Data from: Genetic coupling of female mate choice with polygenic ecological divergence facilitates stickleback speciation

Rachael A. Bay, Matthew E. Arnegard, Gina L. Conte, Jacob Best, Nicole L. Bedford, Shaugnessy R. McCann, Matthew E. Dubin, Yingguang Frank Chan, Felicity C. Jones, David M. Kingsley, Dolph Schluter & Catherine L. Peichel
Ecological speciation with gene flow is widespread in nature, but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, “genetic coupling”) can facilitate speciation. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic...

Data from: Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment

Paul F. Gugger, Christina T. Liang, Victoria L. Sork, Paul Hodgskiss & Jessica W. Wright
Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, both in current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single-nucleotide polymorphisms from...

Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Victor C. Mason, Gang Li, Patrick Minx, Jurgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L. Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen & William J. Murphy
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal...

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  • University of California System
  • University of California, Berkeley
  • University of California, Davis
  • University of California Los Angeles
  • University of California, Riverside
  • Cornell University
  • University of Minnesota
  • Southwest Fisheries Science Center
  • University of British Columbia
  • University of California, Santa Cruz