38 Works

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Human activity reduces niche partitioning among three widespread mesocarnivores

Justine A. Smith, Austen C. Thomas, Taal Levi, Yiwei Wang & Christopher C. Wilmers
Anthropogenic disturbances can constrain the realized niche space of wildlife by inducing avoidance behaviors and altering community dynamics. Human activity might contribute to reduced partitioning of niche space by carnivores that consume similar resources, both by promoting tolerant species while also altering behavior of species (e.g. activity patterns). We investigated the influence of anthropogenic disturbance on habitat and dietary niche breadth and overlap among competing carnivores, and explored if altered resource partitioning could be explained...

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: Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations

Shuangshuang Liu, Jared Streich, Justin O. Borevitz, Kevin J. Rice, Tingting Li, Bo Li & Kent J. Bradford
Intraspecific trait variation within natural populations (i.e. intra‐population trait variation, IPTV) is the basic source for selection and can have significant ecological consequences. Higher IPTV may increase a population's niche breath and benefit interspecies competition under a resource‐limited environment, thus affecting the ability of a species to move into novel habitats. However, the reciprocal influences of variation in environmental conditions and phenotypic trait expression in spreading plant populations are not clearly defined. We propose that...

Data from: Using geometric morphometric visualizations of directional selection gradients to investigate morphological differentiation

Timothy D. Weaver & Philipp Gunz
Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between...

Data from: Experimentally-induced variation in neuroendocrine processes affects male reproductive behavior, sperm characteristics, and social interactions

Bridget M. Nugent, Kelly A. Stiver, Hans A. Hofmann & Suzanne H. Alonzo
While extensive research has focused on how social interactions evolve, the fitness consequences of the neuroendocrine mechanisms underlying these interactions have rarely been documented, especially in the wild. Here, we measure how the neuroendocrine mechanisms underlying male behavior affecting mating success and sperm competition in the ocellated wrasse (Symphodus ocellatus). In this species, males exhibit three alternative reproductive types. ‘Nesting males’ provide parental care, defend territories, and form cooperative associations with unrelated ‘satellites’, who cheat...

Data from: Phenotypic integration between claw and toepad traits promotes microhabitat specialization in the Anolis adaptive radiation

Michael L. Yuan, Marvalee H. Wake & Ian J. Wang
The performance of an organism in its environment frequently depends more on its composite phenotype than on individual phenotypic traits. Thus, understanding environmental adaptation requires investigating patterns of covariation across functionally-related traits. The replicated adaptive radiations of Greater Antillean Anolis lizards are characterized by ecological and morphological convergence, thus providing an opportunity to examine the role of multiple phenotypes in microhabitat adaptation. Here, we examine integrated claw and toepad morphological evolution in relation to habitat...

Data from: Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: a simulation study

Luca Sciuchetti, Christophe Dufresnes, Elisa Cavoto, Alan Brelsford & Nicolas Perrin
Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane’s rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin’s corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex-linked markers. From our simulations, X-Y incompatibilities generate steep clines for both...

Data from: Annual flower strips support pollinators and potentially enhance red clover seed yield

, Ola Lundin & Riccardo Bommarco
1. Ecological intensification provides opportunity to increase agricultural productivity while minimizing negative environmental impacts, by supporting ecosystem services such as crop pollination and biological pest control. For this we need to develop targeted management solutions that provide critical resources to service-providing organisms at the right time and place. 2. We tested whether annual strips of early flowering phacelia Phacelia tanacetifolia support pollinators and natural enemies of seed weevils Protapion spp., by attracting and offering nectar...

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: 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: 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: Genome-wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus)

Devaughn Fraser, Alice Mouton, Laurel E.K. Serieys, Steve Cole, Scott Carver, Sue Vandewoude, Michael Lappin, Seth P.D. Riley, Robert Wayne & Laurel E. K. Serieys
Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten non-target predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR-related effects on genome wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity, and both adaptive and innate immune function. Further, we...

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: Effects of diet on cranial morphology and biting ability in musteloid mammals

Chris J. Law, Emma Duran, Nancy Hung, Ekai Richards, Isaac Santillan & Rita S. Mehta
Size and shape are often considered important variables that lead to variation in performance. In studies of feeding, size‐corrected metrics of the skull are often used as proxies of biting performance; however, few studies have examined the relationship between cranial shape in its entirety and estimated bite force across species and how dietary ecologies may affect these variables differently. Here, we used geometric morphometric and phylogenetic comparative approaches to examine relationships between cranial morphology and...

Data from: Range-wide populations of a long-distance migratory songbird converge during stopover in the tropics

Camila Gomez, Sara L. Guerrero, Alyssa M. FitzGerald, Nicholas J. Bayly, Keith A. Hobson & Carlos Daniel Cadena
Geographic convergence during migration influences the extent to which animal populations may experience carry-over effects across periods of the annual cycle. When most individuals of a population share geographic areas during a given period, carry-over effects are likely stronger than when individuals occupy multiple areas. We used genetic data and stable isotope (δ2H) measurements from feathers and claws to describe the likely breeding and wintering geographic origins of a long-distance migratory songbird (Gray-cheeked Thrush, Catharus...

Data from: Disease and climate effects on individuals drive post-reintroduction population dynamics of an endangered amphibian

Maxwell B. Joseph & Roland A. Knapp
The emergence of novel pathogens often has dramatic negative effects on previously unexposed host populations. Subsequent disease can drive populations and even species to extinction. After establishment in populations, pathogens can continue to affect host dynamics, influencing the success or failure of species recovery efforts. However, quantifying the effect of pathogens on host populations in the wild is challenging because individual hosts and their pathogens are difficult to observe. Here we use long-term mark-recapture data...

Data from: Cumulative reproductive costs on current reproduction in a wild polytocous mammal

Svenja B. Kroeger, Daniel T. Blumstein, Kenneth B. Armitage, Jane M. Reid, Julien G.A. Martin & Julien G. A. Martin
The cumulative cost of reproduction hypothesis predicts that reproductive costs accumulate over an individual’s reproductive lifespan. While short-term costs have been extensively explored, the prevalence of cumulative long-term costs and the circumstances under which such costs occur alongside or instead of short-term costs, are far from clear. Indeed, few studies have simultaneously tested for both short-term and cumulative long-term reproductive costs in natural populations. Even in mammals, comparatively little is known about cumulative effects of...

Data from: Missing the people for the trees: identifying coupled natural-human system feedbacks driving the ecology of Lyme disease

Andrew J. MacDonald, Ashley E. Larsen & Andrew J. Plantinga
1. Infectious diseases are rapidly emerging and many are increasing in incidence across the globe. Processes of land-use change, notably habitat loss and fragmentation, have been widely implicated in emergence and spread of zoonoses such as Lyme disease, yet evidence remains equivocal. 2. Here we discuss and apply an innovative approach from the social sciences, instrumental variables, that seeks to tease out causality from observational data. Using this approach, we revisit the effect of forest...

Data from: Phylogenetic comparative analysis supports aposematic colouration–body size association in millipede assassins (Hemiptera: Reduviidae: Ectrichodiinae)

Michael Forthman & Christiane Weirauch
The diversity of colour patterns and its importance in interactions with the environment make colouration in animals an intriguing research focus. Aposematic colouration is positively correlated with body size in certain groups of animals, suggesting that warning colours are more effective or that crypsis is harder to achieve in larger animals. Surprisingly, this relationship has not been recovered in studies investigating insects, which may have been confounded by a focus on aposematic taxa that are...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of California System
  • University of California, Berkeley
  • University of Kansas
  • Stanford University
  • University of Aberdeen
  • University of Minnesota
  • University of Melbourne
  • National Autonomous University of Mexico
  • University of Hawaii at Manoa
  • Chinese Academy of Sciences